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PDBsum entry 3dc5

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Oxidoreductase PDB id
3dc5
Jmol
Contents
Protein chains
194 a.a.
Ligands
MLI
Metals
_MN ×2
Waters ×420
HEADER    OXIDOREDUCTASE                          03-JUN-08   3DC5
TITLE     CRYSTAL STRUCTURE OF A MANGANESE SUPEROXIDE DISMUTASES FROM
TITLE    2 CAENORHABDITIS ELEGANS
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: SUPEROXIDE DISMUTASE [MN] 2;
COMPND   3 CHAIN: A, C;
COMPND   4 EC: 1.15.1.1;
COMPND   5 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS;
SOURCE   3 ORGANISM_COMMON: NEMATODE;
SOURCE   4 ORGANISM_TAXID: 6239;
SOURCE   5 GENE: SOD-3, C08A9.1;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: OX326A;
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PTRC-99A
KEYWDS    ALPHA HAIRPIN N DOMAIN, ALPHA/BETA C DOMAIN, OXIDOREDUCTASE,
KEYWDS   2 MANGANESE, METAL-BINDING, MITOCHONDRION, TRANSIT PEPTIDE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    C.H.TRINH,T.HUNTER,E.E.STEWART,S.E.V.PHILLIPS,G.J.HUNTER
REVDAT   2   13-JUL-11 3DC5    1       VERSN
REVDAT   1   09-JUN-09 3DC5    0
JRNL        AUTH   C.H.TRINH,T.HUNTER,E.E.STEWART,S.E.PHILLIPS,G.J.HUNTER
JRNL        TITL   PURIFICATION, CRYSTALLIZATION AND X-RAY STRUCTURES OF THE
JRNL        TITL 2 TWO MANGANESE SUPEROXIDE DISMUTASES FROM CAENORHABDITIS
JRNL        TITL 3 ELEGANS
JRNL        REF    ACTA CRYSTALLOGR.,SECT.F      V.  64  1110 2008
JRNL        REFN                   ESSN 1744-3091
JRNL        PMID   19052361
JRNL        DOI    10.1107/S1744309108037056
REMARK   2
REMARK   2 RESOLUTION.    1.70 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0005
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) : 1.70
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 44.07
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 95.8
REMARK   3   NUMBER OF REFLECTIONS             : 49346
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) : 0.191
REMARK   3   R VALUE            (WORKING SET) : 0.189
REMARK   3   FREE R VALUE                     : 0.226
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 2502
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) : 1.70
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.74
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 3348
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 95.46
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2670
REMARK   3   BIN FREE R VALUE SET COUNT          : 209
REMARK   3   BIN FREE R VALUE                    : 0.2820
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3138
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 9
REMARK   3   SOLVENT ATOMS            : 420
REMARK   3
REMARK   3  B VALUES.
REMARK   3   B VALUE TYPE : LIKELY RESIDUAL
REMARK   3   FROM WILSON PLOT           (A**2) : 21.40
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 19.40
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 0.06000
REMARK   3    B22 (A**2) : 0.06000
REMARK   3    B33 (A**2) : -0.13000
REMARK   3    B12 (A**2) : 0.00000
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): 0.110
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.109
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.073
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.923
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.956
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.941
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  3230 ; 0.013 ; 0.021
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  4377 ; 1.398 ; 1.928
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   387 ; 4.430 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   160 ;30.043 ;25.000
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   553 ;11.321 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    10 ;11.874 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   459 ; 0.101 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2478 ; 0.006 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1646 ; 0.209 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2219 ; 0.307 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   332 ; 0.121 ; 0.200
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    61 ; 0.167 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    27 ; 0.081 ; 0.200
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):  2014 ; 0.855 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3102 ; 1.149 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1440 ; 2.022 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1275 ; 3.029 ; 4.500
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  : 2
REMARK   3
REMARK   3   TLS GROUP : 1
REMARK   3    NUMBER OF COMPONENTS GROUP : 1
REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI
REMARK   3    RESIDUE RANGE :   A     1        A   194
REMARK   3    ORIGIN FOR THE GROUP (A):  26.7870   5.9450  -0.8920
REMARK   3    T TENSOR
REMARK   3      T11:  -0.0266 T22:  -0.0706
REMARK   3      T33:   0.1460 T12:   0.0261
REMARK   3      T13:   0.0351 T23:   0.0249
REMARK   3    L TENSOR
REMARK   3      L11:   1.3733 L22:   1.7851
REMARK   3      L33:   1.4371 L12:   0.1860
REMARK   3      L13:   0.0404 L23:  -0.7409
REMARK   3    S TENSOR
REMARK   3      S11:   0.0009 S12:  -0.0416 S13:  -0.1054
REMARK   3      S21:  -0.1452 S22:  -0.1550 S23:  -0.3853
REMARK   3      S31:   0.2663 S32:   0.1384 S33:   0.1541
REMARK   3
REMARK   3   TLS GROUP : 2
REMARK   3    NUMBER OF COMPONENTS GROUP : 1
REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI
REMARK   3    RESIDUE RANGE :   C     0        C   194
REMARK   3    ORIGIN FOR THE GROUP (A):  -8.7530  -2.5360  14.1280
REMARK   3    T TENSOR
REMARK   3      T11:  -0.0634 T22:  -0.0166
REMARK   3      T33:   0.1348 T12:   0.0006
REMARK   3      T13:   0.0675 T23:   0.0609
REMARK   3    L TENSOR
REMARK   3      L11:   1.3820 L22:   1.2766
REMARK   3      L33:   0.8784 L12:  -0.1126
REMARK   3      L13:   0.1410 L23:  -0.3000
REMARK   3    S TENSOR
REMARK   3      S11:   0.0228 S12:  -0.2551 S13:  -0.0911
REMARK   3      S21:   0.1849 S22:   0.0616 S23:   0.3050
REMARK   3      S31:  -0.0412 S32:  -0.1624 S33:  -0.0844
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 RIDING
REMARK   3  POSITIONS
REMARK   4
REMARK   4 3DC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUN-08.
REMARK 100 THE RCSB ID CODE IS RCSB047853.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 25-MAY-07
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 9.2
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : DIAMOND
REMARK 200  BEAMLINE                       : I03
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.060
REMARK 200  MONOCHROMATOR                  : SI (111) DOUBLE CRYSTAL
REMARK 200  OPTICS                         : MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALA
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 49346
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.700
REMARK 200  RESOLUTION RANGE LOW       (A) : 44.070
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 96.2
REMARK 200  DATA REDUNDANCY                : 3.700
REMARK 200  R MERGE                    (I) : 0.07600
REMARK 200  R SYM                      (I) : 0.07600
REMARK 200   FOR THE DATA SET  : 5.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.79
REMARK 200  COMPLETENESS FOR SHELL     (%) : 95.8
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.60
REMARK 200  R MERGE FOR SHELL          (I) : 0.36400
REMARK 200  R SYM FOR SHELL            (I) : 0.36400
REMARK 200   FOR SHELL         : 2.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 1N0J
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 51.63
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.7M AMMONIUM SULPHATE, 0.1M BICINE,
REMARK 280  PH9.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z+1/2
REMARK 290       3555   -Y+1/2,X+1/2,Z+1/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4
REMARK 290       7555   Y,X,-Z
REMARK 290       8555   -Y,-X,-Z+1/2
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 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       68.01550
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       40.89000
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       40.89000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       34.00775
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       40.89000
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       40.89000
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000      102.02325
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       40.89000
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       40.89000
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       34.00775
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       40.89000
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       40.89000
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000      102.02325
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       68.01550
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 7930 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 33160 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.2 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C
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 350   BIOMT1   2  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT2   2  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375      HOH C 197  LIES ON A SPECIAL POSITION.
REMARK 375      HOH A 199  LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     MET A     0
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470   M RES CSSEQI  ATOMS
REMARK 470     LYS A   1    CG   CD   CE   NZ
REMARK 470     LYS A  90    CG   CD   CE   NZ
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    ASN A 141     -120.17     53.13
REMARK 500    TYR A 161      -12.47   -145.45
REMARK 500    LYS A 166     -130.39     51.12
REMARK 500    ASN C 141     -120.41     49.73
REMARK 500    TYR C 161      -18.03   -147.81
REMARK 500    LYS C 166     -134.16     51.17
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 A 314        DISTANCE =  5.11 ANGSTROMS
REMARK 525    HOH A 319        DISTANCE =  5.05 ANGSTROMS
REMARK 525    HOH A 388        DISTANCE =  5.32 ANGSTROMS
REMARK 525    HOH C 319        DISTANCE =  5.02 ANGSTROMS
REMARK 525    HOH C 321        DISTANCE =  5.01 ANGSTROMS
REMARK 525    HOH C 388        DISTANCE =  5.08 ANGSTROMS
REMARK 525    HOH C 396        DISTANCE =  5.98 ANGSTROMS
REMARK 525    HOH C 398        DISTANCE =  8.14 ANGSTROMS
REMARK 525    HOH C 400        DISTANCE =  5.18 ANGSTROMS
REMARK 525    HOH C 402        DISTANCE =  5.16 ANGSTROMS
REMARK 525    HOH C 412        DISTANCE =  5.26 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                              MN A 195  MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 155   OD1
REMARK 620 2 HIS A  26   NE2  82.8
REMARK 620 3 HIS A  74   NE2 112.7  97.6
REMARK 620 4 HIS A 159   NE2 122.7  90.7 124.6
REMARK 620 5 HOH A 197   O    89.7 171.0  89.8  89.2
REMARK 620 N                    1     2     3     4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MN C 195  MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP C 155   OD1
REMARK 620 2 HIS C  26   NE2  85.0
REMARK 620 3 HIS C  74   NE2 109.1  95.4
REMARK 620 4 HIS C 159   NE2 119.0  89.3 131.9
REMARK 620 5 HOH C 196   O    84.1 168.3  92.2  92.2
REMARK 620 N                    1     2     3     4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 195
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 195
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 196
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3DC6   RELATED DB: PDB
DBREF  3DC5 A    1   194  UNP    P41977   SODM2_CAEEL     25    218
DBREF  3DC5 C    1   194  UNP    P41977   SODM2_CAEEL     25    218
SEQADV 3DC5 MET A    0  UNP  P41977              INITIATING METHIONINE
SEQADV 3DC5 MET C    0  UNP  P41977              INITIATING METHIONINE
SEQRES   1 A  195  MET LYS HIS THR LEU PRO ASP LEU PRO PHE ASP TYR ALA
SEQRES   2 A  195  ASP LEU GLU PRO VAL ILE SER HIS GLU ILE MET GLN LEU
SEQRES   3 A  195  HIS HIS GLN LYS HIS HIS ALA THR TYR VAL ASN ASN LEU
SEQRES   4 A  195  ASN GLN ILE GLU GLU LYS LEU HIS GLU ALA VAL SER LYS
SEQRES   5 A  195  GLY ASN LEU LYS GLU ALA ILE ALA LEU GLN PRO ALA LEU
SEQRES   6 A  195  LYS PHE ASN GLY GLY GLY HIS ILE ASN HIS SER ILE PHE
SEQRES   7 A  195  TRP THR ASN LEU ALA LYS ASP GLY GLY GLU PRO SER LYS
SEQRES   8 A  195  GLU LEU MET ASP THR ILE LYS ARG ASP PHE GLY SER LEU
SEQRES   9 A  195  ASP ASN LEU GLN LYS ARG LEU SER ASP ILE THR ILE ALA
SEQRES  10 A  195  VAL GLN GLY SER GLY TRP GLY TRP LEU GLY TYR CYS LYS
SEQRES  11 A  195  LYS ASP LYS ILE LEU LYS ILE ALA THR CYS ALA ASN GLN
SEQRES  12 A  195  ASP PRO LEU GLU GLY MET VAL PRO LEU PHE GLY ILE ASP
SEQRES  13 A  195  VAL TRP GLU HIS ALA TYR TYR LEU GLN TYR LYS ASN VAL
SEQRES  14 A  195  ARG PRO ASP TYR VAL HIS ALA ILE TRP LYS ILE ALA ASN
SEQRES  15 A  195  TRP LYS ASN ILE SER GLU ARG PHE ALA ASN ALA ARG GLN
SEQRES   1 C  195  MET LYS HIS THR LEU PRO ASP LEU PRO PHE ASP TYR ALA
SEQRES   2 C  195  ASP LEU GLU PRO VAL ILE SER HIS GLU ILE MET GLN LEU
SEQRES   3 C  195  HIS HIS GLN LYS HIS HIS ALA THR TYR VAL ASN ASN LEU
SEQRES   4 C  195  ASN GLN ILE GLU GLU LYS LEU HIS GLU ALA VAL SER LYS
SEQRES   5 C  195  GLY ASN LEU LYS GLU ALA ILE ALA LEU GLN PRO ALA LEU
SEQRES   6 C  195  LYS PHE ASN GLY GLY GLY HIS ILE ASN HIS SER ILE PHE
SEQRES   7 C  195  TRP THR ASN LEU ALA LYS ASP GLY GLY GLU PRO SER LYS
SEQRES   8 C  195  GLU LEU MET ASP THR ILE LYS ARG ASP PHE GLY SER LEU
SEQRES   9 C  195  ASP ASN LEU GLN LYS ARG LEU SER ASP ILE THR ILE ALA
SEQRES  10 C  195  VAL GLN GLY SER GLY TRP GLY TRP LEU GLY TYR CYS LYS
SEQRES  11 C  195  LYS ASP LYS ILE LEU LYS ILE ALA THR CYS ALA ASN GLN
SEQRES  12 C  195  ASP PRO LEU GLU GLY MET VAL PRO LEU PHE GLY ILE ASP
SEQRES  13 C  195  VAL TRP GLU HIS ALA TYR TYR LEU GLN TYR LYS ASN VAL
SEQRES  14 C  195  ARG PRO ASP TYR VAL HIS ALA ILE TRP LYS ILE ALA ASN
SEQRES  15 C  195  TRP LYS ASN ILE SER GLU ARG PHE ALA ASN ALA ARG GLN
HET     MN  A 195       1
HET     MN  C 195       1
HET    MLI  A 196       7
HETNAM      MN MANGANESE (II) ION
HETNAM     MLI MALONATE ION
FORMUL   3   MN    2(MN 2+)
FORMUL   5  MLI    C3 H2 O4 2-
FORMUL   6  HOH   *420(H2 O)
HELIX    1   1 SER A   19  LYS A   29  1                                  11
HELIX    2   2 LYS A   29  GLY A   52  1                                  24
HELIX    3   3 ASN A   53  LEU A   60  1                                   8
HELIX    4   4 LEU A   60  ASN A   80  1                                  21
HELIX    5   5 SER A   89  GLY A  101  1                                  13
HELIX    6   6 SER A  102  ALA A  116  1                                  15
HELIX    7   7 TRP A  157  ALA A  160  5                                   4
HELIX    8   8 TYR A  161  LYS A  166  1                                   6
HELIX    9   9 VAL A  168  TRP A  177  1                                  10
HELIX   10  10 LYS A  178  ALA A  180  5                                   3
HELIX   11  11 ASN A  181  GLN A  194  1                                  14
HELIX   12  12 SER C   19  LYS C   29  1                                  11
HELIX   13  13 LYS C   29  GLY C   52  1                                  24
HELIX   14  14 ASN C   53  LEU C   60  1                                   8
HELIX   15  15 LEU C   60  ASN C   80  1                                  21
HELIX   16  16 SER C   89  GLY C  101  1                                  13
HELIX   17  17 SER C  102  ALA C  116  1                                  15
HELIX   18  18 TRP C  157  ALA C  160  5                                   4
HELIX   19  19 TYR C  161  LYS C  166  1                                   6
HELIX   20  20 VAL C  168  TRP C  177  1                                  10
HELIX   21  21 LYS C  178  ALA C  180  5                                   3
HELIX   22  22 ASN C  181  ARG C  193  1                                  13
SHEET    1   A 3 ILE A 133  ALA A 140  0
SHEET    2   A 3 GLY A 121  CYS A 128 -1  N  TRP A 124   O  ALA A 137
SHEET    3   A 3 VAL A 149  ASP A 155 -1  O  VAL A 149   N  TYR A 127
SHEET    1   B 3 ILE C 133  ALA C 140  0
SHEET    2   B 3 GLY C 121  CYS C 128 -1  N  GLY C 126   O  LYS C 135
SHEET    3   B 3 VAL C 149  ASP C 155 -1  O  LEU C 151   N  LEU C 125
LINK         OD1 ASP A 155                MN    MN A 195     1555   1555  2.05
LINK         OD1 ASP C 155                MN    MN C 195     1555   1555  2.07
LINK         NE2 HIS A  26                MN    MN A 195     1555   1555  2.24
LINK         NE2 HIS C  26                MN    MN C 195     1555   1555  2.22
LINK         NE2 HIS A  74                MN    MN A 195     1555   1555  2.18
LINK         NE2 HIS C  74                MN    MN C 195     1555   1555  2.19
LINK         NE2 HIS A 159                MN    MN A 195     1555   1555  2.23
LINK         NE2 HIS C 159                MN    MN C 195     1555   1555  2.13
LINK        MN    MN A 195                 O   HOH A 197     1555   1555  2.25
LINK        MN    MN C 195                 O   HOH C 196     1555   1555  2.26
CISPEP   1 GLU A   15    PRO A   16          0         2.67
CISPEP   2 GLU C   15    PRO C   16          0         2.87
SITE     1 AC1  4 HIS C  26  HIS C  74  ASP C 155  HIS C 159
SITE     1 AC2  4 HIS A  26  HIS A  74  ASP A 155  HIS A 159
SITE     1 AC3  1 ASN A 167
CRYST1   81.780   81.780  136.031  90.00  90.00  90.00 P 41 21 2    16
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      0.012228  0.000000  0.000000        0.00000
SCALE2      0.000000  0.012228  0.000000        0.00000
SCALE3      0.000000  0.000000  0.007351        0.00000
      
PROCHECK
Go to PROCHECK summary
 References