HEADER HYDROLASE 02-DEC-08 2ZWB
TITLE NEUTRON CRYSTAL STRUCTURE OF WILD TYPE HUMAN LYSOZYME IN D2O
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSOZYME C;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C;
COMPND 5 EC: 3.2.1.17;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPIC9
KEYWDS NEUTRON D2O HYDROGEN HYDRATION, HYDROLASE, AMYLOID, AMYLOIDOSIS,
KEYWDS 2 ANTIMICROBIAL, BACTERIOLYTIC ENZYME, DISEASE MUTATION, GLYCOSIDASE
EXPDTA NEUTRON DIFFRACTION
AUTHOR K.CHIBA-KAMOSHIDA,T.MATSUI,T.CHATAKE,T.OHHARA,A.OSTERMANN,I.TANAKA,
AUTHOR 2 K.YUTANI,N.NIIMURA
REVDAT 5 01-NOV-23 2ZWB 1 REMARK
REVDAT 4 07-MAR-18 2ZWB 1 REMARK
REVDAT 3 11-OCT-17 2ZWB 1 REMARK
REVDAT 2 13-JUL-11 2ZWB 1 VERSN
REVDAT 1 08-DEC-09 2ZWB 0
JRNL AUTH K.CHIBA-KAMOSHIDA,T.MATSUI,T.CHATAKE,T.OHHARA,A.OSTERMANN,
JRNL AUTH 2 I.TANAKA,K.YUTANI,N.NIIMURA
JRNL TITL SITE-SPECIFIC SOFTENING OF PEPTIDE BONDS BY LOCALIZED
JRNL TITL 2 DEUTERIUM OBSERVED BY NEUTRON CRYSTALLOGRAPHY OF HUMAN
JRNL TITL 3 LYSOZYME
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 0.000
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1
REMARK 3 NUMBER OF REFLECTIONS : 10947
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.223
REMARK 3 FREE R VALUE : 0.247
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600
REMARK 3 FREE R VALUE TEST SET COUNT : 1089
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 : 1029
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 65
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.30
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
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) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : 10.00
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 : PROTEIN_KC4.PARAMDEFHARDNLYS
REMARK 3 PARAMETER FILE 2 : PARNEUTRON.SOLKC3
REMARK 3 PARAMETER FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2ZWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-DEC-08.
REMARK 100 THE DEPOSITION ID IS D_1000028506.
REMARK 230
REMARK 230 EXPERIMENTAL DETAILS
REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION
REMARK 230 DATE OF DATA COLLECTION : 01-JUL-01
REMARK 230 TEMPERATURE (KELVIN) : 298.0
REMARK 230 PH : 4.30
REMARK 230 NUMBER OF CRYSTALS USED : 1
REMARK 230
REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR
REMARK 230 BEAMLINE : NULL
REMARK 230 WAVELENGTH OR RANGE (A) : 2.88
REMARK 230 MONOCHROMATOR : ELASTICALLY-BENT PERFECT SILICON
REMARK 230 MONOCHROMATOR
REMARK 230 OPTICS : NULL
REMARK 230
REMARK 230 DETECTOR TYPE : IMAGE PLATE
REMARK 230 DETECTOR MANUFACTURER : JAERI BIX-3
REMARK 230 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 230 DATA SCALING SOFTWARE : SCALEPACK
REMARK 230
REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 25514
REMARK 230 RESOLUTION RANGE HIGH (A) : 1.200
REMARK 230 RESOLUTION RANGE LOW (A) : 100.000
REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 230
REMARK 230 OVERALL.
REMARK 230 COMPLETENESS FOR RANGE (%) : 69.0
REMARK 230 DATA REDUNDANCY : 2.900
REMARK 230 R MERGE (I) : 0.21100
REMARK 230 R SYM (I) : NULL
REMARK 230 <I/SIGMA(I)> FOR THE DATA SET : 3.8940
REMARK 230
REMARK 230 IN THE HIGHEST RESOLUTION SHELL.
REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20
REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24
REMARK 230 COMPLETENESS FOR SHELL (%) : NULL
REMARK 230 DATA REDUNDANCY IN SHELL : NULL
REMARK 230 R MERGE FOR SHELL (I) : 0.49100
REMARK 230 R SYM FOR SHELL (I) : NULL
REMARK 230 <I/SIGMA(I)> FOR SHELL : 1.110
REMARK 230
REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 230 SOFTWARE USED : CNS
REMARK 230 STARTING MODEL: PDB ENTRY 3FE0
REMARK 230
REMARK 230 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.30(PD), SMALL TUBES, TEMPERATURE
REMARK 280 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
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 16.91250
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.48250
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.44150
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.48250
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.91250
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.44150
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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 DD2 ASP A 67 DG1 THR A 70 1.03
REMARK 500 DE2 GLU A 35 D1 DOD A 145 1.41
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3FE0 RELATED DB: PDB
REMARK 900 THE SAME PROTEIN OBSERVED BY X-RAY. THE CRYSTAL WAS OBTAINED FROM
REMARK 900 THE SAME BATCH AS THIS CRYSTAL FOR NEUTRON EXPERIMENT.
DBREF 2ZWB A 1 130 UNP P61626 LYSC_HUMAN 19 148
SEQRES 1 A 130 LYS VAL PHE GLU ARG CYS GLU LEU ALA ARG THR LEU LYS
SEQRES 2 A 130 ARG LEU GLY MET ASP GLY TYR ARG GLY ILE SER LEU ALA
SEQRES 3 A 130 ASN TRP MET CYS LEU ALA LYS TRP GLU SER GLY TYR ASN
SEQRES 4 A 130 THR ARG ALA THR ASN TYR ASN ALA GLY ASP ARG SER THR
SEQRES 5 A 130 ASP TYR GLY ILE PHE GLN ILE ASN SER ARG TYR TRP CYS
SEQRES 6 A 130 ASN ASP GLY LYS THR PRO GLY ALA VAL ASN ALA CYS HIS
SEQRES 7 A 130 LEU SER CYS SER ALA LEU LEU GLN ASP ASN ILE ALA ASP
SEQRES 8 A 130 ALA VAL ALA CYS ALA LYS ARG VAL VAL ARG ASP PRO GLN
SEQRES 9 A 130 GLY ILE ARG ALA TRP VAL ALA TRP ARG ASN ARG CYS GLN
SEQRES 10 A 130 ASN ARG ASP VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL
FORMUL 2 DOD *65(D2 O)
HELIX 1 1 GLU A 4 LEU A 15 1 12
HELIX 2 2 GLY A 19 ILE A 23 5 5
HELIX 3 3 SER A 24 GLY A 37 1 14
HELIX 4 4 SER A 80 GLN A 86 5 7
HELIX 5 5 ILE A 89 VAL A 100 1 12
HELIX 6 6 GLN A 104 ALA A 108 5 5
HELIX 7 7 TRP A 109 CYS A 116 1 8
HELIX 8 8 VAL A 121 VAL A 125 5 5
SHEET 1 A 3 THR A 43 TYR A 45 0
SHEET 2 A 3 THR A 52 TYR A 54 -1 O ASP A 53 N ASN A 44
SHEET 3 A 3 ILE A 59 ASN A 60 -1 O ILE A 59 N TYR A 54
SSBOND 1 CYS A 6 CYS A 128 1555 1555 2.12
SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.04
SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.08
SSBOND 4 CYS A 77 CYS A 95 1555 1555 2.09
CRYST1 33.825 56.883 60.965 90.00 90.00 90.00 P 21 21 21 4
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 0.029564 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017580 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016403 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
