HEADER HYDROLASE 05-FEB-01 1I20 TITLE MUTANT HUMAN LYSOZYME (A92D) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.17; 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_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PERI8811 KEYWDS CALCIUM BINDING SITE, MUTANT HUMAN LYSOZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.KUROKI REVDAT 6 30-OCT-24 1I20 1 REMARK REVDAT 5 25-OCT-23 1I20 1 REMARK REVDAT 4 10-NOV-21 1I20 1 SEQADV SSBOND REVDAT 3 24-FEB-09 1I20 1 VERSN REVDAT 2 31-DEC-02 1I20 1 REMARK REVDAT 1 28-FEB-01 1I20 0 JRNL AUTH R.KUROKI,K.YUTANI JRNL TITL STRUCTURAL AND THERMODYNAMIC RESPONSES OF MUTATIONS AT A JRNL TITL 2 CA2+ BINDING SITE ENGINEERED INTO HUMAN LYSOZYME. JRNL REF J.BIOL.CHEM. V. 273 34310 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9852096 JRNL DOI 10.1074/JBC.273.51.34310 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.KUROKI,K.NITTA,K.YUTANI REMARK 1 TITL THERMODYNAMIC CHANGES IN THE BINDING OF CA2+ TO A MUTANT REMARK 1 TITL 2 HUMAN LYSOZYME (D86/92). ENTHALPY-ENTROPY COMPENSATION REMARK 1 TITL 3 OBSERVED UPON CA2+ BINDING TO PROTEINS. REMARK 1 REF J.BIOL.CHEM. V. 267 24297 1992 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.KUROKI,S.KAWAKITA,H.NAKAMURA,K.YUTANI REMARK 1 TITL ENTROPIC STABILIZATION OF A MUTANT HUMAN LYSOZYME INDUCED BY REMARK 1 TITL 2 CALCIUM BINDING REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 89 6803 1992 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.INAKA,R.KUROKI,M.KIKUCHI,M.MATSUSHIMA REMARK 1 TITL CRYSTAL STRUCTURES OF THE APO- AND HOLOMUTANT HUMAN REMARK 1 TITL 2 LYSOZYMES WITH AN INTRODUCED CA2+ BINDING SITE REMARK 1 REF J.BIOL.CHEM. V. 266 20666 1991 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.KUROKI,Y.TANIYAMA,C.SEKO,H.NAKAMURA,M.KIKUCHI,M.IKEHARA REMARK 1 TITL DESIGN AND CREATION OF A CA2+ BINDING SITE IN HUMAN LYSOZYME REMARK 1 TITL 2 TO ENHANCE STRUCTURAL STABILITY REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 86 6903 1989 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.0 REMARK 3 NUMBER OF REFLECTIONS : 8000 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.164 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 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1640 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1032 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; 1.000 ; 1056 REMARK 3 BOND ANGLES (DEGREES) : 2.539 ; 1.250 ; 1427 REMARK 3 TORSION ANGLES (DEGREES) : 15.878; 0.000 ; 634 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.012 ; 2.000 ; 29 REMARK 3 GENERAL PLANES (A) : 0.012 ; 6.000 ; 157 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : 0.017 ; 10.000; 16 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 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 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I20 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 6.00 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SDMS REMARK 200 DATA SCALING SOFTWARE : SDMS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35220 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: TNT REMARK 200 STARTING MODEL: PDB ENTRY 2LHM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PHOSPHATE, SODIUM CHLORIDE, CALCIUM REMARK 280 CHLORIDE, PH 6.00, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277.0K 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 28.53500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.92500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.31500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.92500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.53500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.31500 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: 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 OE2 GLU A 4 O HOH A 252 0.71 REMARK 500 CG ASP A 102 O HOH A 254 1.56 REMARK 500 CD GLU A 4 O HOH A 252 1.65 REMARK 500 O HOH A 255 O HOH A 275 1.66 REMARK 500 OD1 ASP A 102 O HOH A 254 1.74 REMARK 500 OD1 ASP A 91 O HOH A 281 1.82 REMARK 500 OD2 ASP A 102 O HOH A 254 2.02 REMARK 500 O HOH A 172 O HOH A 282 2.10 REMARK 500 NH1 ARG A 41 O HOH A 265 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 18 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 TYR A 20 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 TYR A 20 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 TYR A 38 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 TYR A 45 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 49 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 53 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 53 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP A 67 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 67 CB - CG - OD2 ANGL. DEV. = -9.1 DEGREES REMARK 500 LEU A 79 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 ASP A 87 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 91 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 101 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 102 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LZ1 RELATED DB: PDB REMARK 900 1LZ1 CONTAINS NATURAL HUMAN LYSOZYME REMARK 900 RELATED ID: 1I1Z RELATED DB: PDB REMARK 900 1I1Z CONTAINS MUTANT HUMAN LYSOZYME (Q86D) REMARK 900 RELATED ID: 1I22 RELATED DB: PDB REMARK 900 1I22 CONTAINS MUTANT HUMAN LYSOZYME (A83K/Q86D/A92D) REMARK 900 RELATED ID: 2LHM RELATED DB: PDB REMARK 900 2LHM CONTAINS MUTANT HUMAN LYSOZYME (APO-Q86D/A92D) REMARK 900 RELATED ID: 3LHM RELATED DB: PDB REMARK 900 3LHM CONTAINS MUTANT HUMAN LYSOZYME (HOLO-Q86D/A92D) DBREF 1I20 A 1 130 UNP P61626 LYSC_HUMAN 19 148 SEQADV 1I20 ASP A 92 UNP P61626 ALA 110 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 ASP 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 HOH *82(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 N ILE A 59 O TYR A 54 SSBOND 1 CYS A 6 CYS A 128 1555 1555 1.95 SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.00 SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.03 SSBOND 4 CYS A 77 CYS A 95 1555 1555 1.98 CRYST1 57.070 60.630 33.850 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 0.017522 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029542 0.00000