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PDBsum entry 3rz4

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Hydrolase PDB id
3rz4
Jmol
Contents
Protein chain
129 a.a.
Ligands
EPE
Waters ×115
HEADER    HYDROLASE                               11-MAY-11   3RZ4
TITLE     HEN EGG-WHITE LYSOZYME IN HEPES BUFFER AT PH 7.5
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: LYSOZYME C;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UNP RESIDUES 19-147;
COMPND   5 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D IV;
COMPND   6 EC: 3.2.1.17
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
SOURCE   3 ORGANISM_COMMON: BANTAM,CHICKENS;
SOURCE   4 ORGANISM_TAXID: 9031
KEYWDS    HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    K.PERETOLTCHINE,S.BRYSON,E.F.PAI
REVDAT   1   25-MAY-11 3RZ4    0
JRNL        AUTH   K.PERETOLTCHINE,S.BRYSON,E.F.PAI
JRNL        TITL   HEN EGG-WHITE LYSOZYME IN HEPES BUFFER AT PH 7.5
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION.    1.80 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : ENGH & HUBER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 17.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 40.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 98.2
REMARK   3   NUMBER OF REFLECTIONS             : 10538
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.208
REMARK   3   FREE R VALUE                     : 0.223
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : 523
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : NULL
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 1001
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 15
REMARK   3   SOLVENT ATOMS            : 115
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 25.38
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -1.14600
REMARK   3    B22 (A**2) : -1.14600
REMARK   3    B33 (A**2) : 2.29100
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 COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : NULL
REMARK   3   BOND ANGLES            (DEGREES) : NULL
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : 1.001 ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 1.527 ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : 1.502 ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 2.321 ; NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : NULL
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3RZ4 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-11.
REMARK 100 THE RCSB ID CODE IS RCSB065556.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 09-MAR-11
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 7.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : ROTATING ANODE
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU MICROMAX-007 HF
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : NI FILTER
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : MAR SCANNER 345 MM PLATE
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 10731
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.800
REMARK 200  RESOLUTION RANGE LOW       (A) : 17.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.0
REMARK 200  DATA REDUNDANCY                : 6.500
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.09900
REMARK 200   FOR THE DATA SET  : 31.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.85
REMARK 200  COMPLETENESS FOR SHELL     (%) : 86.7
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.78
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.09900
REMARK 200   FOR SHELL         : 4.450
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 3FE0
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 35.53
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M POTASSIUM SODIUM TARTRATE
REMARK 280  TETRAHYDRATE, 0.1M HEPES SODIUM, PH 7.5, VAPOR DIFFUSION, HANGING
REMARK 280  DROP, TEMPERATURE 373K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+1/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+3/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/4
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       18.35000
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       38.60000
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       38.60000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       27.52500
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       38.60000
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       38.60000
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000        9.17500
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       38.60000
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       38.60000
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       27.52500
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       38.60000
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       38.60000
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000        9.17500
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       18.35000
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 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 A 221  LIES ON A SPECIAL POSITION.
REMARK 375      HOH A 180  LIES ON A SPECIAL POSITION.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 3380
DBREF  3RZ4 A    1   129  UNP    P00698   LYSC_CHICK      19    147
SEQRES   1 A  129  LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
SEQRES   2 A  129  ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
SEQRES   3 A  129  ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
SEQRES   4 A  129  THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
SEQRES   5 A  129  TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
SEQRES   6 A  129  ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
SEQRES   7 A  129  PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
SEQRES   8 A  129  VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
SEQRES   9 A  129  MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
SEQRES  10 A  129  THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
HET    EPE  A3380      15
HETNAM     EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HETSYN     EPE HEPES
FORMUL   2  EPE    C8 H18 N2 O4 S
FORMUL   3  HOH   *115(H2 O)
HELIX    1   1 GLY A    4  HIS A   15  1                                  12
HELIX    2   2 ASN A   19  TYR A   23  5                                   5
HELIX    3   3 SER A   24  ASN A   37  1                                  14
HELIX    4   4 PRO A   79  SER A   85  5                                   7
HELIX    5   5 ILE A   88  SER A  100  1                                  13
HELIX    6   6 ASP A  101  GLY A  102  5                                   2
HELIX    7   7 ASN A  103  ALA A  107  5                                   5
HELIX    8   8 TRP A  108  CYS A  115  1                                   8
HELIX    9   9 ASP A  119  ARG A  125  5                                   7
SHEET    1   A 3 THR A  43  ARG A  45  0
SHEET    2   A 3 THR A  51  TYR A  53 -1  O  ASP A  52   N  ASN A  44
SHEET    3   A 3 ILE A  58  ASN A  59 -1  O  ILE A  58   N  TYR A  53
SSBOND   1 CYS A    6    CYS A  127                          1555   1555  2.03
SSBOND   2 CYS A   30    CYS A  115                          1555   1555  2.03
SSBOND   3 CYS A   64    CYS A   80                          1555   1555  2.03
SSBOND   4 CYS A   76    CYS A   94                          1555   1555  2.03
SITE     1 AC1 12 ARG A  21  GLU A  35  ASN A  46  THR A  47
SITE     2 AC1 12 ASP A  52  GLN A  57  TRP A 108  VAL A 109
SITE     3 AC1 12 GLY A 126  HOH A 173  HOH A 226  HOH A 228
CRYST1   77.200   77.200   36.700  90.00  90.00  90.00 P 43 21 2     8
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      0.012953  0.000000  0.000000        0.00000
SCALE2      0.000000  0.012953  0.000000        0.00000
SCALE3      0.000000  0.000000  0.027248        0.00000
      
PROCHECK
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