PDB Short entry for 1WQO HEADER HYDROLASE 09-FEB-98 1WQO TITLE CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF TITLE 2 HUMAN LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MURAMIDASE; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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: SACCHAROMYCES CEREVISIAE; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: AH22R-; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEL125 KEYWDS HYDROLASE (O-GLYCOSYL), GLYCOSIDASE, BACTERIOLYTIC ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.YAMAGATA,M.KUBOTA,Y.SUMIKAWA,J.FUNAHASHI,S.FUJII,K.YUTANI REVDAT 3 03-NOV-21 1WQO 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1WQO 1 VERSN REVDAT 1 01-JUL-98 1WQO 0 JRNL AUTH Y.YAMAGATA,M.KUBOTA,Y.SUMIKAWA,J.FUNAHASHI,K.TAKANO,S.FUJII, JRNL AUTH 2 K.YUTANI JRNL TITL CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL JRNL TITL 2 STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS JRNL TITL 3 OF SIX TYROSINE --> PHENYLALANINE MUTANTS. JRNL REF BIOCHEMISTRY V. 37 9355 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9649316 JRNL DOI 10.1021/BI980431I REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.TAKANO,Y.YAMAGATA,S.FUJII,K.YUTANI REMARK 1 TITL CONTRIBUTION OF THE HYDROPHOBIC EFFECT TO THE STABILITY OF REMARK 1 TITL 2 HUMAN LYSOZYME: CALORIMETRIC STUDIES AND X-RAY STRUCTURAL REMARK 1 TITL 3 ANALYSES OF THE NINE VALINE TO ALANINE MUTANTS REMARK 1 REF BIOCHEMISTRY V. 36 688 1997 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.TAKANO,J.FUNAHASHI,Y.YAMAGATA,S.FUJII,K.YUTANI REMARK 1 TITL CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN REMARK 1 TITL 2 TO THE CONFORMATIONAL STABILITY REMARK 1 REF J.MOL.BIOL. V. 274 132 1997 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.TAKANO,K.OGASAHARA,H.KANEDA,Y.YAMAGATA,S.FUJII,E.KANAYA, REMARK 1 AUTH 2 M.KIKUCHI,M.OOBATAKE,K.YUTANI REMARK 1 TITL CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF REMARK 1 TITL 2 HUMAN LYSOZYME: CALORIMETRIC STUDIES AND X-RAY STRUCTURAL REMARK 1 TITL 3 ANALYSIS OF THE FIVE ISOLEUCINE TO VALINE MUTANTS REMARK 1 REF J.MOL.BIOL. V. 254 62 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 10803 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) : 0.170 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1282 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 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 : 1028 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.540 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.340 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 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 1WQO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-96 REMARK 200 TEMPERATURE (KELVIN) : 283 REMARK 200 PH : 4.5 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48488 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.586 REMARK 200 RESOLUTION RANGE LOW (A) : 61.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE MAP REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: WILD-TYPE OF HUMAN LYSOZYME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M TO 1.9M NACL, 20MM ACETATE, PH REMARK 280 4.5 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 28.32500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.87000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.87000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.51000 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 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 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 NA A 131 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 61 O REMARK 620 2 CYS A 65 O 88.2 REMARK 620 3 VAL A 74 O 107.4 103.5 REMARK 620 4 HOH A 137 O 88.5 92.4 157.6 REMARK 620 5 HOH A 158 O 147.5 120.0 82.8 75.5 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 NA A 131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 133 DBREF 1WQO A 1 130 UNP P61626 LYSC_HUMAN 19 148 SEQADV 1WQO PHE A 38 UNP P61626 TYR 56 ENGINEERED MUTATION 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 PHE 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 HET NA A 131 1 HET CL A 132 1 HET CL A 133 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NA NA 1+ FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *221(H2 O) HELIX 1 1 ARG A 5 ARG A 14 1 10 HELIX 2 2 TYR A 20 GLY A 22 5 3 HELIX 3 3 LEU A 25 SER A 36 1 12 HELIX 4 4 CYS A 81 LEU A 85 5 5 HELIX 5 5 ALA A 90 ARG A 101 1 12 HELIX 6 6 GLY A 105 ALA A 108 5 4 HELIX 7 7 VAL A 110 ARG A 115 1 6 HELIX 8 8 VAL A 121 TYR A 124 5 4 SHEET 1 A 2 THR A 43 ASN A 46 0 SHEET 2 A 2 SER A 51 TYR A 54 -1 N ASP A 53 O ASN A 44 SSBOND 1 CYS A 6 CYS A 128 1555 1555 2.03 SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.02 SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.03 SSBOND 4 CYS A 77 CYS A 95 1555 1555 2.02 LINK O SER A 61 NA NA A 131 1555 1555 2.02 LINK O CYS A 65 NA NA A 131 1555 1555 2.20 LINK O VAL A 74 NA NA A 131 1555 1555 2.51 LINK NA NA A 131 O HOH A 137 1555 1555 2.36 LINK NA NA A 131 O HOH A 158 1555 1555 2.26 SITE 1 AC1 7 SER A 61 CYS A 65 ASN A 66 ALA A 73 SITE 2 AC1 7 VAL A 74 HOH A 137 HOH A 158 SITE 1 AC2 2 ASN A 27 ASN A 66 SITE 1 AC3 4 SER A 80 ARG A 107 TRP A 112 HOH A 170 CRYST1 56.650 61.020 33.740 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 0.017652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029638 0.00000