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PDBsum entry 3do0

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Hydrolase PDB id
3do0
Jmol
Contents
Protein chain
316 a.a.
Ligands
VAL-LYS
Metals
_CA ×4
_ZN
Waters ×185
HEADER    HYDROLASE                               03-JUL-08   3DO0
TITLE     THERMOLYSIN BY CLASSICAL HANGING DROP METHOD AFTER HIGH X-
TITLE    2 RAY DOSE ON ESRF ID14-2 BEAMLINE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: THERMOLYSIN;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: THERMOSTABLE NEUTRAL PROTEINASE;
COMPND   5 EC: 3.4.24.27
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: BACILLUS THERMOPROTEOLYTICUS;
SOURCE   3 ORGANISM_TAXID: 1427
KEYWDS    HYDROLASE, METALLOPROTEINASE, CALCIUM, METAL-BINDING,
KEYWDS   2 METALLOPROTEASE, PROTEASE, SECRETED, ZINC, ZYMOGEN
EXPDTA    X-RAY DIFFRACTION
AUTHOR    E.PECHKOVA,S.K.TRIPATHI,C.NICOLINI
REVDAT   1   07-JUL-09 3DO0    0
JRNL        AUTH   E.PECHKOVA,S.K.TRIPATHI,C.NICOLINI
JRNL        TITL   RADIATION DAMAGE IN PROTEIN STRUCTURAL
JRNL        TITL 2 CHARACTERIZATION BY SYNCHROTRON RADIATION: STATE OF
JRNL        TITL 3 THE ART AND NANOTECHNOLOGY-BASED PERSPECTIVE
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    1.36 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0019
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 80.32
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 57.5
REMARK   3   NUMBER OF REFLECTIONS             : 40360
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.224
REMARK   3   R VALUE            (WORKING SET) : 0.223
REMARK   3   FREE R VALUE                     : 0.255
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 2047
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 20
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.36
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.40
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 5
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 10.00
REMARK   3   BIN R VALUE           (WORKING SET) : 0.6600
REMARK   3   BIN FREE R VALUE SET COUNT          : NULL
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2479
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 22
REMARK   3   SOLVENT ATOMS            : 185
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 22.18
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.55000
REMARK   3    B22 (A**2) : -0.55000
REMARK   3    B33 (A**2) : 0.82000
REMARK   3    B12 (A**2) : -0.27000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): 0.116
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.113
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.076
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.988
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.949
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.938
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2562 ; 0.011 ; 0.021
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  3496 ; 1.202 ; 1.924
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   328 ; 5.373 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   126 ;32.552 ;24.444
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   369 ;13.927 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    10 ;15.301 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   371 ; 0.085 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2046 ; 0.004 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1307 ; 0.220 ; 0.300
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  1770 ; 0.318 ; 0.500
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   323 ; 0.227 ; 0.500
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):    17 ; 0.048 ; 0.500
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    37 ; 0.241 ; 0.300
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    22 ; 0.375 ; 0.500
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  1627 ; 0.966 ; 2.000
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  2563 ; 1.486 ; 3.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1085 ; 1.118 ; 2.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):   933 ; 1.544 ; 3.000
REMARK   3
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  NCS RESTRAINTS STATISTICS
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.20
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK   3  RIDING POSITIONS
REMARK   4
REMARK   4 3DO0 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUL-08.
REMARK 100 THE RCSB ID CODE IS RCSB048274.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 15-MAY-07
REMARK 200  TEMPERATURE           (KELVIN) : 110
REMARK 200  PH                             : 6.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : ID14-2
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.93
REMARK 200  MONOCHROMATOR                  : DIAMOND (111)
REMARK 200  OPTICS                         : TOROIDAL MIRROR
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 4
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALA
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 64386
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.360
REMARK 200  RESOLUTION RANGE LOW       (A) : 80.322
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 81.2
REMARK 200  DATA REDUNDANCY                : 5.300
REMARK 200  R MERGE                    (I) : 0.27500
REMARK 200  R SYM                      (I) : 0.27500
REMARK 200   FOR THE DATA SET  : 2.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.38
REMARK 200  COMPLETENESS FOR SHELL     (%) : 24.1
REMARK 200  DATA REDUNDANCY IN SHELL       : 1.50
REMARK 200  R MERGE FOR SHELL          (I) : 0.15400
REMARK 200  R SYM FOR SHELL            (I) : 0.15357
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 47.03
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: DMSO, AMMONIUM SULFATE, MES,
REMARK 280  HANGING DROP, 293K, PH6.0, VAPOR DIFFUSION, HANGING DROP
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -Y,X-Y,Z+1/3
REMARK 290       3555   -X+Y,-X,Z+2/3
REMARK 290       4555   -X,-Y,Z+1/2
REMARK 290       5555   Y,-X+Y,Z+5/6
REMARK 290       6555   X-Y,X,Z+1/6
REMARK 290       7555   Y,X,-Z+1/3
REMARK 290       8555   X-Y,-Y,-Z
REMARK 290       9555   -X,-X+Y,-Z+2/3
REMARK 290      10555   -Y,-X,-Z+5/6
REMARK 290      11555   -X+Y,Y,-Z+1/2
REMARK 290      12555   X,X-Y,-Z+1/6
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       42.86667
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       85.73333
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       64.30000
REMARK 290   SMTRY1   5  0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   5 -0.866025  0.500000  0.000000        0.00000
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000      107.16667
REMARK 290   SMTRY1   6  0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   6  0.866025  0.500000  0.000000        0.00000
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       21.43333
REMARK 290   SMTRY1   7 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   7  0.866025  0.500000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       42.86667
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   9 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   9 -0.866025  0.500000  0.000000        0.00000
REMARK 290   SMTRY3   9  0.000000  0.000000 -1.000000       85.73333
REMARK 290   SMTRY1  10  0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2  10 -0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3  10  0.000000  0.000000 -1.000000      107.16667
REMARK 290   SMTRY1  11 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2  11  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3  11  0.000000  0.000000 -1.000000       64.30000
REMARK 290   SMTRY1  12  0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2  12  0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3  12  0.000000  0.000000 -1.000000       21.43333
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   O    HOH A  1118     O    HOH A  1149              1.44
REMARK 500   O    HOH A  1059     O    HOH A  1167              1.63
REMARK 500   O    HOH A  1067     O    HOH A  1141              1.90
REMARK 500   O    HOH A  1056     O    HOH A  1165              1.97
REMARK 500   O    HOH A  1013     O    HOH A  1026              2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   O    HOH A  1088     O    HOH A  1116     8566     1.61
REMARK 500   O    HOH A  1161     O    HOH A  1150     6655     1.76
REMARK 500   O    HOH A  1101     O    HOH A  1129     8666     1.88
REMARK 500   O    HOH A  1107     O    HOH A  1138     6655     2.00
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    SER A  25       92.25   -166.50
REMARK 500    THR A  26      -61.19     73.14
REMARK 500    LEU A  30       80.03    -67.07
REMARK 500    SER A  92     -175.02     57.89
REMARK 500    SER A 107     -164.13     60.35
REMARK 500    ASN A 111       51.13    -91.37
REMARK 500    THR A 152      -95.41   -122.54
REMARK 500    ASN A 159     -142.70     51.19
REMARK 500    THR A 194       79.27     37.10
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A1180        DISTANCE =  6.13 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620  (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620  SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 403  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A  57   OD1
REMARK 620 2 ASP A  57   OD2  52.8
REMARK 620 3 ASP A  59   OD1 124.3  71.6
REMARK 620 4 GLN A  61   O    94.9  90.5  86.1
REMARK 620 5 HOH A1016   O    87.4  81.9  83.3 168.4
REMARK 620 6 HOH A1014   O    83.1 135.0 151.7  84.4 107.1
REMARK 620 7 HOH A1021   O   162.5 143.9  72.5  90.7  90.4  81.0
REMARK 620 N                    1     2     3     4     5     6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 401  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 138   OD2
REMARK 620 2 GLU A 177   OE1  78.3
REMARK 620 3 GLU A 177   OE2 125.4  48.1
REMARK 620 4 ASP A 185   OD1 158.4 122.8  74.9
REMARK 620 5 GLU A 187   O    83.5 145.1 145.6  80.3
REMARK 620 6 GLU A 190   OE1  81.7 127.7 120.6  81.0  77.7
REMARK 620 7 GLU A 190   OE2  95.8  84.6  73.3  82.8 127.0  50.1
REMARK 620 8 HOH A1005   O   102.5  75.4  76.0  88.6  79.9 156.6 149.3
REMARK 620 N                    1     2     3     4     5     6     7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              ZN A 405  ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 142   NE2
REMARK 620 2 HIS A 146   NE2 105.6
REMARK 620 3 GLU A 166   OE2 123.3  90.8
REMARK 620 N                    1     2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 402  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 177   OE2
REMARK 620 2 ASN A 183   O    89.6
REMARK 620 3 ASP A 185   OD2  89.7  91.3
REMARK 620 4 GLU A 190   OE2  86.4 170.8  80.3
REMARK 620 5 HOH A1019   O   169.2  93.7 100.5  91.7
REMARK 620 6 HOH A1030   O    88.1  93.2 175.0  95.0  81.5
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 404  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 TYR A 193   O
REMARK 620 2 THR A 194   O    73.2
REMARK 620 3 THR A 194   OG1  75.0  69.2
REMARK 620 4 ILE A 197   O   155.1  82.6 101.8
REMARK 620 5 ASP A 200   OD1 123.6 134.4  75.1  77.8
REMARK 620 6 HOH A1009   O    85.4 149.2 126.8 114.4  76.0
REMARK 620 7 HOH A1051   O    74.9  78.1 140.6  95.0 143.8  75.0
REMARK 620 N                    1     2     3     4     5     6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 401
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 403
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 404
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 405
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VAL A 1001
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYS A 1002
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1KEI   RELATED DB: PDB
REMARK 900 THERMOLYSIN
REMARK 900 RELATED ID: 3DNZ   RELATED DB: PDB
REMARK 900 THERMOLYSIN
REMARK 900 RELATED ID: 3DO1   RELATED DB: PDB
REMARK 900 THERMOLYSIN
REMARK 900 RELATED ID: 3DO2   RELATED DB: PDB
REMARK 900 THERMOLYSIN
DBREF  3DO0 A    1   316  UNP    P00800   THER_BACTH     233    548
SEQRES   1 A  316  ILE THR GLY THR SER THR VAL GLY VAL GLY ARG GLY VAL
SEQRES   2 A  316  LEU GLY ASP GLN LYS ASN ILE ASN THR THR TYR SER THR
SEQRES   3 A  316  TYR TYR TYR LEU GLN ASP ASN THR ARG GLY ASN GLY ILE
SEQRES   4 A  316  PHE THR TYR ASP ALA LYS TYR ARG THR THR LEU PRO GLY
SEQRES   5 A  316  SER LEU TRP ALA ASP ALA ASP ASN GLN PHE PHE ALA SER
SEQRES   6 A  316  TYR ASP ALA PRO ALA VAL ASP ALA HIS TYR TYR ALA GLY
SEQRES   7 A  316  VAL THR TYR ASP TYR TYR LYS ASN VAL HIS ASN ARG LEU
SEQRES   8 A  316  SER TYR ASP GLY ASN ASN ALA ALA ILE ARG SER SER VAL
SEQRES   9 A  316  HIS TYR SER GLN GLY TYR ASN ASN ALA PHE TRP ASN GLY
SEQRES  10 A  316  SER GLN MET VAL TYR GLY ASP GLY ASP GLY GLN THR PHE
SEQRES  11 A  316  ILE PRO LEU SER GLY GLY ILE ASP VAL VAL ALA HIS GLU
SEQRES  12 A  316  LEU THR HIS ALA VAL THR ASP TYR THR ALA GLY LEU ILE
SEQRES  13 A  316  TYR GLN ASN GLU SER GLY ALA ILE ASN GLU ALA ILE SER
SEQRES  14 A  316  ASP ILE PHE GLY THR LEU VAL GLU PHE TYR ALA ASN LYS
SEQRES  15 A  316  ASN PRO ASP TRP GLU ILE GLY GLU ASP VAL TYR THR PRO
SEQRES  16 A  316  GLY ILE SER GLY ASP SER LEU ARG SER MET SER ASP PRO
SEQRES  17 A  316  ALA LYS TYR GLY ASP PRO ASP HIS TYR SER LYS ARG TYR
SEQRES  18 A  316  THR GLY THR GLN ASP ASN GLY GLY VAL HIS ILE ASN SER
SEQRES  19 A  316  GLY ILE ILE ASN LYS ALA ALA TYR LEU ILE SER GLN GLY
SEQRES  20 A  316  GLY THR HIS TYR GLY VAL SER VAL VAL GLY ILE GLY ARG
SEQRES  21 A  316  ASP LYS LEU GLY LYS ILE PHE TYR ARG ALA LEU THR GLN
SEQRES  22 A  316  TYR LEU THR PRO THR SER ASN PHE SER GLN LEU ARG ALA
SEQRES  23 A  316  ALA ALA VAL GLN SER ALA THR ASP LEU TYR GLY SER THR
SEQRES  24 A  316  SER GLN GLU VAL ALA SER VAL LYS GLN ALA PHE ASP ALA
SEQRES  25 A  316  VAL GLY VAL LYS
HET     CA  A 401       1
HET     CA  A 402       1
HET     CA  A 403       1
HET     CA  A 404       1
HET     ZN  A 405       1
HET    VAL  A1001       7
HET    LYS  A1002      10
HETNAM      CA CALCIUM ION
HETNAM      ZN ZINC ION
HETNAM     VAL VALINE
HETNAM     LYS LYSINE
FORMUL   2   CA    4(CA 2+)
FORMUL   6   ZN    ZN 2+
FORMUL   7  VAL    C5 H11 N O2
FORMUL   8  LYS    C6 H15 N2 O2 1+
FORMUL   9  HOH   *185(H2 O)
HELIX    1   1 ALA A   64  TYR A   66  5                                   3
HELIX    2   2 ASP A   67  ASN A   89  1                                  23
HELIX    3   3 PRO A  132  GLY A  135  5                                   4
HELIX    4   4 GLY A  136  THR A  152  1                                  17
HELIX    5   5 GLN A  158  ASN A  181  1                                  24
HELIX    6   6 ASP A  207  GLY A  212  5                                   6
HELIX    7   7 HIS A  216  ARG A  220  5                                   5
HELIX    8   8 THR A  224  VAL A  230  1                                   7
HELIX    9   9 ASN A  233  GLY A  247  1                                  15
HELIX   10  10 GLY A  259  TYR A  274  1                                  16
HELIX   11  11 ASN A  280  GLY A  297  1                                  18
HELIX   12  12 SER A  300  VAL A  313  1                                  14
SHEET    1   A 5 ALA A  56  ASP A  57  0
SHEET    2   A 5 TYR A  28  TYR A  29 -1  N  TYR A  28   O  ASP A  57
SHEET    3   A 5 GLN A  17  TYR A  24 -1  N  THR A  23   O  TYR A  29
SHEET    4   A 5 THR A   4  ARG A  11 -1  N  THR A   4   O  TYR A  24
SHEET    5   A 5 GLN A  61  PHE A  62  1  O  PHE A  62   N  VAL A   9
SHEET    1   B 3 GLN A  31  ASP A  32  0
SHEET    2   B 3 ILE A  39  ASP A  43 -1  O  ILE A  39   N  ASP A  32
SHEET    3   B 3 SER A  53  LEU A  54 -1  O  SER A  53   N  ASP A  43
SHEET    1   C 5 GLN A  31  ASP A  32  0
SHEET    2   C 5 ILE A  39  ASP A  43 -1  O  ILE A  39   N  ASP A  32
SHEET    3   C 5 ILE A 100  VAL A 104  1  O  ILE A 100   N  PHE A  40
SHEET    4   C 5 MET A 120  TYR A 122  1  O  MET A 120   N  ARG A 101
SHEET    5   C 5 ALA A 113  TRP A 115 -1  N  PHE A 114   O  VAL A 121
SHEET    1   D 2 GLU A 187  ILE A 188  0
SHEET    2   D 2 ARG A 203  SER A 204 -1  O  ARG A 203   N  ILE A 188
SHEET    1   E 2 GLY A 248  HIS A 250  0
SHEET    2   E 2 VAL A 253  VAL A 255 -1  O  VAL A 255   N  GLY A 248
LINK         OD1 ASP A  57                CA    CA A 403     1555   1555  2.36
LINK         OD2 ASP A  57                CA    CA A 403     1555   1555  2.58
LINK         OD1 ASP A  59                CA    CA A 403     1555   1555  2.44
LINK         O   GLN A  61                CA    CA A 403     1555   1555  2.37
LINK         OD2 ASP A 138                CA    CA A 401     1555   1555  2.40
LINK         NE2 HIS A 142                ZN    ZN A 405     1555   1555  2.05
LINK         NE2 HIS A 146                ZN    ZN A 405     1555   1555  2.08
LINK         OE2 GLU A 166                ZN    ZN A 405     1555   1555  2.01
LINK         OE1 GLU A 177                CA    CA A 401     1555   1555  2.48
LINK         OE2 GLU A 177                CA    CA A 401     1555   1555  2.84
LINK         OE2 GLU A 177                CA    CA A 402     1555   1555  2.40
LINK         O   ASN A 183                CA    CA A 402     1555   1555  2.41
LINK         OD1 ASP A 185                CA    CA A 401     1555   1555  2.55
LINK         OD2 ASP A 185                CA    CA A 402     1555   1555  2.46
LINK         O   GLU A 187                CA    CA A 401     1555   1555  2.38
LINK         OE1 GLU A 190                CA    CA A 401     1555   1555  2.60
LINK         OE2 GLU A 190                CA    CA A 401     1555   1555  2.55
LINK         OE2 GLU A 190                CA    CA A 402     1555   1555  2.32
LINK         O   TYR A 193                CA    CA A 404     1555   1555  2.39
LINK         O   THR A 194                CA    CA A 404     1555   1555  2.47
LINK         OG1 THR A 194                CA    CA A 404     1555   1555  2.48
LINK         O   ILE A 197                CA    CA A 404     1555   1555  2.36
LINK         OD1 ASP A 200                CA    CA A 404     1555   1555  2.36
LINK        CA    CA A 401                 O   HOH A1005     1555   1555  2.39
LINK        CA    CA A 402                 O   HOH A1019     1555   1555  2.56
LINK        CA    CA A 402                 O   HOH A1030     1555   1555  2.36
LINK        CA    CA A 403                 O   HOH A1016     1555   1555  2.38
LINK        CA    CA A 403                 O   HOH A1014     1555   1555  2.39
LINK        CA    CA A 403                 O   HOH A1021     1555   1555  2.36
LINK        CA    CA A 404                 O   HOH A1009     1555   1555  2.46
LINK        CA    CA A 404                 O   HOH A1051     1555   1555  2.73
LINK         C   VAL A1001                 N   LYS A1002     1555   1555  1.34
CISPEP   1 LEU A   50    PRO A   51          0        -1.97
SITE     1 AC1  6 ASP A 138  GLU A 177  ASP A 185  GLU A 187
SITE     2 AC1  6 GLU A 190  HOH A1005
SITE     1 AC2  6 GLU A 177  ASN A 183  ASP A 185  GLU A 190
SITE     2 AC2  6 HOH A1019  HOH A1030
SITE     1 AC3  6 ASP A  57  ASP A  59  GLN A  61  HOH A1014
SITE     2 AC3  6 HOH A1016  HOH A1021
SITE     1 AC4  6 TYR A 193  THR A 194  ILE A 197  ASP A 200
SITE     2 AC4  6 HOH A1009  HOH A1051
SITE     1 AC5  3 HIS A 142  HIS A 146  GLU A 166
SITE     1 AC6  7 ASN A 112  ALA A 113  GLU A 143  ARG A 203
SITE     2 AC6  7 HIS A 231  LYS A1002  HOH A1185
SITE     1 AC7  5 ASN A 111  ASN A 112  PHE A 130  HIS A 231
SITE     2 AC7  5 HOH A1164
CRYST1   92.724   92.724  128.600  90.00  90.00 120.00 P 61 2 2     12
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.010785  0.006227  0.000000        0.00000
SCALE2      0.000000  0.012453  0.000000        0.00000
SCALE3      0.000000  0.000000  0.007776        0.00000
      
PROCHECK
Go to PROCHECK summary
 References

 

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