HEADER HYDROLASE 26-JUN-00 1GBY
TITLE CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME SUBSTITUTED AT THE SURFACE
TITLE 2 POSITIONS
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_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PERI8602
KEYWDS SURFACE MUTANT, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.FUNAHASHI,K.TAKANO,Y.YAMAGATA,K.YUTANI
REVDAT 7 27-DEC-23 1GBY 1 REMARK
REVDAT 6 10-NOV-21 1GBY 1 REMARK SEQADV LINK
REVDAT 5 04-OCT-17 1GBY 1 REMARK
REVDAT 4 24-FEB-09 1GBY 1 VERSN
REVDAT 3 01-APR-03 1GBY 1 JRNL
REVDAT 2 28-JAN-03 1GBY 1 REMARK
REVDAT 1 27-JUL-00 1GBY 0
JRNL AUTH J.FUNAHASHI,K.TAKANO,Y.YAMAGATA,K.YUTANI
JRNL TITL ROLE OF SURFACE HYDROPHOBIC RESIDUES IN THE CONFORMATIONAL
JRNL TITL 2 STABILITY OF HUMAN LYSOZYME AT THREE DIFFERENT POSITIONS.
JRNL REF BIOCHEMISTRY V. 39 14448 2000
JRNL REFN ISSN 0006-2960
JRNL PMID 11087397
JRNL DOI 10.1021/BI0015717
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.FUNAHASHI,K.TAKANO,Y.YAMAGATA,K.YUTANI
REMARK 1 TITL CONTRIBUTION OF AMINO ACID SUBSTITUTIONS AT TWO DIFFERENT
REMARK 1 TITL 2 INTERIOR POSITIONS TO THE CONFORMATIONAL STABILITY OF HUMAN
REMARK 1 TITL 3 LYSOZYME
REMARK 1 REF PROTEIN ENG. V. 12 841 1999
REMARK 1 REFN ISSN 0269-2139
REMARK 1 DOI 10.1093/PROTEIN/12.10.841
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)) : NULL
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 65.1
REMARK 3 NUMBER OF REFLECTIONS : 7154
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) : 0.166
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 : 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 : 1030
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 1
REMARK 3 SOLVENT ATOMS : 273
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) : 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 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 1GBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-00.
REMARK 100 THE DEPOSITION ID IS D_1000005021.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-JUL-98
REMARK 200 TEMPERATURE (KELVIN) : 100
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 RU300
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS
REMARK 200 DATA SCALING SOFTWARE : R-AXIS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8483
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 76.0
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.10900
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) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 36.55
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM PHOSPHATE, SODIUM CHLORIDE, PH
REMARK 280 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K
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 28.41000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.51500
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 16.51500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.41000
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
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 TYR A 38 31.65 70.93
REMARK 500
REMARK 500 REMARK: NULL
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 601 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 61 O
REMARK 620 2 CYS A 65 O 87.5
REMARK 620 3 VAL A 74 O 100.1 98.0
REMARK 620 4 HOH A 259 O 87.7 102.6 158.3
REMARK 620 N 1 2 3
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 601
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2MEI RELATED DB: PDB
REMARK 900 I59Y OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GAY RELATED DB: PDB
REMARK 900 V2G OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GAZ RELATED DB: PDB
REMARK 900 V2I OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GB0 RELATED DB: PDB
REMARK 900 V2L OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GB2 RELATED DB: PDB
REMARK 900 V2M OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GB3 RELATED DB: PDB
REMARK 900 V2F OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GB5 RELATED DB: PDB
REMARK 900 V74G OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GB6 RELATED DB: PDB
REMARK 900 V74I OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GB7 RELATED DB: PDB
REMARK 900 V74L OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GB8 RELATED DB: PDB
REMARK 900 V74M OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GB9 RELATED DB: PDB
REMARK 900 V74F OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GBO RELATED DB: PDB
REMARK 900 V110G OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GBW RELATED DB: PDB
REMARK 900 V110I OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GBX RELATED DB: PDB
REMARK 900 V110L OF HUMAN LYSOZYME
REMARK 900 RELATED ID: 1GBZ RELATED DB: PDB
REMARK 900 V110F OF HUMAN LYSOZYME
DBREF 1GBY A 1 130 UNP P61626 LYSC_HUMAN 19 148
SEQADV 1GBY MET A 110 UNP P61626 VAL 128 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 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 MET 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 601 1
HETNAM NA SODIUM ION
FORMUL 2 NA NA 1+
FORMUL 3 HOH *273(H2 O)
HELIX 1 1 GLU A 4 LEU A 15 1 12
HELIX 2 2 SER A 24 GLY A 37 1 14
HELIX 3 3 CYS A 81 GLN A 86 5 6
HELIX 4 4 ILE A 89 ARG A 101 1 13
HELIX 5 5 GLN A 104 ALA A 108 5 5
HELIX 6 6 TRP A 109 CYS A 116 1 8
HELIX 7 7 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 N ASP A 53 O 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 2.04
SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.03
SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.04
SSBOND 4 CYS A 77 CYS A 95 1555 1555 2.02
LINK O SER A 61 NA NA A 601 1554 1555 2.01
LINK O CYS A 65 NA NA A 601 1554 1555 2.11
LINK O VAL A 74 NA NA A 601 1554 1555 2.52
LINK O HOH A 259 NA NA A 601 1554 1555 2.27
SITE 1 AC1 6 SER A 61 CYS A 65 ASN A 66 ALA A 73
SITE 2 AC1 6 VAL A 74 HOH A 259
CRYST1 56.820 60.960 33.030 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 0.017599 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016404 0.000000 0.00000
SCALE3 0.000000 0.000000 0.030276 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
