HEADER HYDROLASE 21-MAY-98 2BQG
TITLE CONTRIBUTION OF HYDROPHOBIC EFFECT TO THE CONFORMATIONAL STABILITY OF
TITLE 2 HUMAN LYSOZYME
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSOZYME;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.2.1.17;
COMPND 5 ENGINEERED: YES;
COMPND 6 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 ENZYME, HYDROLASE, O-GLYCOSYL, ALPHA, BETA, GLYCOSIDASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.TAKANO,Y.YAMAGATA,K.YUTANI
REVDAT 4 03-APR-24 2BQG 1 REMARK
REVDAT 3 03-NOV-21 2BQG 1 SEQADV
REVDAT 2 24-FEB-09 2BQG 1 VERSN
REVDAT 1 12-AUG-98 2BQG 0
JRNL AUTH K.TAKANO,Y.YAMAGATA,K.YUTANI
JRNL TITL A GENERAL RULE FOR THE RELATIONSHIP BETWEEN HYDROPHOBIC
JRNL TITL 2 EFFECT AND CONFORMATIONAL STABILITY OF A PROTEIN: STABILITY
JRNL TITL 3 AND STRUCTURE OF A SERIES OF HYDROPHOBIC MUTANTS OF HUMAN
JRNL TITL 4 LYSOZYME.
JRNL REF J.MOL.BIOL. V. 280 749 1998
JRNL REFN ISSN 0022-2836
JRNL PMID 9677301
JRNL DOI 10.1006/JMBI.1998.1906
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH Y.YAMAGATA,M.KUBOTA,Y.SUMIKAWA,J.FUNAHASHI,K.TAKANO,S.FUJII,
REMARK 1 AUTH 2 K.YUTANI
REMARK 1 TITL CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL
REMARK 1 TITL 2 STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS
REMARK 1 TITL 3 OF SIX TYROSINE--> PHENYLALANINE MUTANTS
REMARK 1 REF BIOCHEMISTRY V. 37 9355 1998
REMARK 1 REFN ISSN 0006-2960
REMARK 1 REFERENCE 2
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 3
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 4
REMARK 1 AUTH J.FUNAHASHI,K.TAKANO,K.OGASAHARA,Y.YAMAGATA,K.YUTANI
REMARK 1 TITL THE STRUCTURE, STABILITY, AND FOLDING PROCESS OF
REMARK 1 TITL 2 AMYLOIDOGENIC MUTANT HUMAN LYSOZYME
REMARK 1 REF J.BIOCHEM.(TOKYO) V. 120 1216 1996
REMARK 1 REFN ISSN 0021-924X
REMARK 1 REFERENCE 5
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 1 REFERENCE 6
REMARK 1 AUTH R.KUROKI,K.INAKA,Y.TANIYAMA,S.KIDOKORO,M.MATSUSHIMA,
REMARK 1 AUTH 2 M.KIKUCHI,K.YUTANI
REMARK 1 TITL ENTHALPIC DESTABILIZATION OF A MUTANT HUMAN LYSOZYME LACKING
REMARK 1 TITL 2 A DISULFIDE BRIDGE BETWEEN CYSTEINE-77 AND CYSTEINE-95
REMARK 1 REF BIOCHEMISTRY V. 31 8323 1992
REMARK 1 REFN ISSN 0006-2960
REMARK 1 REFERENCE 7
REMARK 1 AUTH K.INAKA,Y.TANIYAMA,M.KIKUCHI,K.MORIKAWA,M.MATSUSHIMA
REMARK 1 TITL THE CRYSTAL STRUCTURE OF A MUTANT HUMAN LYSOZYME C77/95A
REMARK 1 TITL 2 WITH INCREASED SECRETION EFFICIENCY IN YEAST
REMARK 1 REF J.BIOL.CHEM. V. 266 12599 1991
REMARK 1 REFN ISSN 0021-9258
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
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) (%) : 91.3
REMARK 3 NUMBER OF REFLECTIONS : 10205
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) : 0.171
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) (%) : 77.00
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1059
REMARK 3 BIN R VALUE (WORKING SET) : 0.2400
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 : 1025
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 182
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) : 1.510
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.260
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 2BQG 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_1000177866.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 20-AUG-97
REMARK 200 TEMPERATURE (KELVIN) : 298
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 : 29699
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5
REMARK 200 DATA REDUNDANCY : 2.500
REMARK 200 R MERGE (I) : 0.06100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
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) : 1.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 81.4
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.15600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.100
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS METHOD
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: C77A/C95A OF HUMAN LYSOZYME
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.25
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M TO 1.8M 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 28.50000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.77500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.48000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.77500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.50000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.48000
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
DBREF 2BQG A 1 130 UNP P61626 LYSC_HUMAN 19 148
SEQADV 2BQG ALA A 77 UNP P61626 CYS 95 ENGINEERED MUTATION
SEQADV 2BQG ALA A 95 UNP P61626 CYS 113 ENGINEERED MUTATION
SEQADV 2BQG ALA A 100 UNP P61626 VAL 118 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 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 ALA 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 ALA ALA LYS ARG VAL ALA 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 HOH *182(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 ALA A 100 1 11
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 ARG A 122 TYR A 124 5 3
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 2.04
CRYST1 57.000 60.960 33.550 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 0.017544 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016404 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029806 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
