HEADER HYDROLASE 10-OCT-00 1G12 TITLE ZINC PEPTIDASE FROM GRIFOLA FRONDOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-LYS METALLOENDOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.24.20 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GRIFOLA FRONDOSA; SOURCE 3 ORGANISM_COMMON: FUNGI; SOURCE 4 TISSUE: FRUITING BODY KEYWDS ZINC CORDINATE,METALLOPROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HORI,T.KUMASAKA,M.YAMAMOTO,T.NONAKA,N.TANAKA,Y.HASHIMOTO, AUTHOR 2 T.UEKI,K.TAKIO REVDAT 3 01-APR-03 1G12 1 JRNL REVDAT 2 31-DEC-02 1G12 1 REMARK REVDAT 1 14-MAR-01 1G12 0 JRNL AUTH T.HORI,T.KUMASAKA,M.YAMAMOTO,N.NONAKA,N.TANAKA, JRNL AUTH 2 Y.HASHIMOTO,U.UEKI,K.TAKIO JRNL TITL STRUCTURE OF A NEW 'ASPZINCIN' JRNL TITL 2 METALLOENDOPEPTIDASE FROM GRIFOLA FRONDOSA: JRNL TITL 3 IMPLICATIONS FOR THE CATALYTIC MECHANISM AND JRNL TITL 4 SUBSTRATE SPECIFICITY BASED ON SEVERAL DIFFERENT JRNL TITL 5 CRYSTAL FORMS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 361 2001 JRNL REFN ASTM ABCRE6 DK ISSN 0907-4449 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.3 REMARK 3 NUMBER OF REFLECTIONS : 96644 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 777 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 : 1271 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.06 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 : 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 1G12 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-29) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ . REMARK 100 THE RCSB ID CODE IS RCSB012100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-1998 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS (RIGAKU) REMARK 200 DATA SCALING SOFTWARE : PROCESS (RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96644 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 38.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.19500 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: DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, PH 7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 21.81550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.87850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.81550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.87850 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 42 CB THR A 42 OG1 0.038 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 49 N - CA - C ANGL. DEV. = -7.6 DEGREES REMARK 500 ASP A 67 N - CA - C ANGL. DEV. = -6.9 DEGREES REMARK 500 SER A 72 N - CA - C ANGL. DEV. = -7.1 DEGREES REMARK 500 TYR A 87 N - CA - C ANGL. DEV. = -9.2 DEGREES REMARK 500 GLY A 92 N - CA - C ANGL. DEV. = 8.8 DEGREES REMARK 500 GLY A 98 N - CA - C ANGL. DEV. = 8.1 DEGREES REMARK 500 MET A 144 N - CA - C ANGL. DEV. = 6.5 DEGREES REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 515 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH 534 DISTANCE = 5.26 ANGSTROMS REMARK 525 HOH 579 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH 591 DISTANCE = 7.47 ANGSTROMS REMARK 525 HOH 594 DISTANCE = 5.20 ANGSTROMS REMARK 525 HOH 633 DISTANCE = 5.59 ANGSTROMS REMARK 525 HOH 634 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH 636 DISTANCE = 7.47 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GE5 RELATED DB: PDB REMARK 900 1GE5 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM. REMARK 900 RELATED ID: 1GE6 RELATED DB: PDB REMARK 900 1GE6 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM. REMARK 900 RELATED ID: 1GE7 RELATED DB: PDB REMARK 900 1GE7 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM. DBREF 1G12 A 1 167 UNP P81054 PLMP_GRIFR 1 167 SEQRES 1 A 167 THR TYR ASN GLY CYS SER SER SER GLU GLN SER ALA LEU SEQRES 2 A 167 ALA ALA ALA ALA SER ALA ALA GLN SER TYR VAL ALA GLU SEQRES 3 A 167 SER LEU SER TYR LEU GLN THR HIS THR ALA ALA THR PRO SEQRES 4 A 167 ARG TYR THR THR TRP PHE GLY SER TYR ILE SER SER ARG SEQRES 5 A 167 HIS SER THR VAL LEU GLN HIS TYR THR ASP MET ASN SER SEQRES 6 A 167 ASN ASP PHE SER SER TYR SER PHE ASP CYS THR CYS THR SEQRES 7 A 167 ALA ALA GLY THR PHE ALA TYR VAL TYR PRO ASN ARG PHE SEQRES 8 A 167 GLY THR VAL TYR LEU CYS GLY ALA PHE TRP LYS ALA PRO SEQRES 9 A 167 THR THR GLY THR ASP SER GLN ALA GLY THR LEU VAL HIS SEQRES 10 A 167 GLU SER SER HIS PHE THR ARG ASN GLY GLY THR LYS ASP SEQRES 11 A 167 TYR ALA TYR GLY GLN ALA ALA ALA LYS SER LEU ALA THR SEQRES 12 A 167 MET ASP PRO ASP LYS ALA VAL MET ASN ALA ASP ASN HIS SEQRES 13 A 167 GLU TYR PHE SER GLU ASN ASN PRO ALA GLN SER MODRES 1G12 THR A 42 THR GLYCOSYLATION SITE HET MAN A 900 11 HET ZN A 200 1 HETNAM MAN ALPHA-D-MANNOSE HETNAM ZN ZINC ION FORMUL 2 MAN C6 H12 O6 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *201(H2 O) HELIX 1 1 SER A 6 HIS A 34 1 29 HELIX 2 2 THR A 38 GLY A 46 1 9 HELIX 3 3 ILE A 49 SER A 65 1 17 HELIX 4 4 ASN A 66 ASN A 66 5 1 HELIX 5 5 ASP A 67 TYR A 71 5 5 HELIX 6 6 GLY A 98 ALA A 103 5 6 HELIX 7 7 SER A 110 PHE A 122 1 13 HELIX 8 8 THR A 123 GLY A 126 5 4 HELIX 9 9 TYR A 133 ASP A 145 1 13 HELIX 10 10 ASP A 145 VAL A 150 1 6 HELIX 11 11 ASN A 152 ASN A 162 1 11 SHEET 1 A 4 TYR A 2 ASN A 3 0 SHEET 2 A 4 SER A 72 ASP A 74 1 O PHE A 73 N ASN A 3 SHEET 3 A 4 THR A 93 LEU A 96 1 N VAL A 94 O SER A 72 SHEET 4 A 4 ALA A 84 TYR A 85 -1 O TYR A 85 N TYR A 95 SSBOND 1 CYS A 5 CYS A 75 SSBOND 2 CYS A 77 CYS A 97 LINK OG1 THR A 42 C1 MAN A 900 LINK NE2 HIS A 117 ZN ZN A 200 LINK NE2 HIS A 121 ZN ZN A 200 LINK OD1 ASP A 130 ZN ZN A 200 CISPEP 1 ASN A 163 PRO A 164 0 0.12 CRYST1 43.631 41.757 76.941 90.00 95.48 90.00 C 1 2 1 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 0.022919 0.000000 0.002199 0.00000 SCALE2 0.000000 0.023948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013057 0.00000