HEADER HYDROLASE 04-AUG-04 1WNI TITLE CRYSTAL STRUCTURE OF H2-PROTEINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIMERELYSIN II; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: H2-PROTEINASE, H2 METALLOPROTEINASE; COMPND 5 EC: 3.4.24.53 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRIMERESURUS FLAVOVIRIDIS; SOURCE 3 ORGANISM_TAXID: 88087 KEYWDS METALLOPROTEASE, ZINC, METZINCIN, SNAKE VENOM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.KUMASAKA,M.YAMAMOTO,H.MORIYAMA,N.TANAKA,M.SATO,Y.KATSUBE, AUTHOR 2 Y.YAMAKAWA,T.OMORI-SATOH,S.IWANAGA,T.UEKI REVDAT 3 09-OCT-19 1WNI 1 JRNL REVDAT 2 24-FEB-09 1WNI 1 VERSN REVDAT 1 17-AUG-04 1WNI 0 JRNL AUTH T.KUMASAKA,M.YAMAMOTO,H.MORIYAMA,N.TANAKA,M.SATO,Y.KATSUBE, JRNL AUTH 2 Y.YAMAKAWA,T.OMORI-SATOH,S.IWANAGA,T.UEKI JRNL TITL CRYSTAL STRUCTURE OF H2-PROTEINASE FROM THE VENOM OF JRNL TITL 2 TRIMERESURUS FLAVOVIRIDIS. JRNL REF J.BIOCHEM. V. 119 49 1996 JRNL REFN ISSN 0021-924X JRNL PMID 8907175 JRNL DOI 10.1093/OXFORDJOURNALS.JBCHEM.A021215 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.KUMASAKA,H.TAKEYA,M.YAMAMOTO,Y.YAMAKAWA,T.OMORI-SATOH, REMARK 1 AUTH 2 H.MORIYAMA,N.TANAKA,M.SATO,Y.KATSUBE,S.IWANAGA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDY OF H2-PROTEINASE REMARK 1 TITL 2 FROM THE VENOM OF TRIMERESURUS FLAVOVIRIDIS REMARK 1 REF J.BIOCHEM.(TOKYO) V. 117 929 1995 REMARK 1 REFN ISSN 0021-924X REMARK 1 PMID 8586633 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10635 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) : 0.176 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 : 1581 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 78 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 1WNI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023780. 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 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS REMARK 200 DATA SCALING SOFTWARE : WEIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14262 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06900 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: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 41.15000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.90000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.72500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.90000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.90000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.57500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.90000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.90000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.72500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.90000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.90000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.57500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 41.15000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 1 REMARK 465 ARG A 2 REMARK 465 PRO A 201 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 LEU A 148 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 55 138.76 -171.57 REMARK 500 CYS A 117 -22.89 88.44 REMARK 500 LYS A 155 -36.78 -36.53 REMARK 500 LYS A 175 33.24 -97.52 REMARK 500 ASN A 193 66.08 35.44 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 ZN A 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 142 NE2 REMARK 620 2 HIS A 146 NE2 88.1 REMARK 620 3 HIS A 152 NE2 93.0 94.9 REMARK 620 4 HOH A1011 O 106.4 138.8 121.7 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 ZN A 999 DBREF 1WNI A 1 201 UNP P20165 HR2_TRIFL 1 201 SEQRES 1 A 201 GLN ARG PHE PRO GLN ARG TYR ILE GLU LEU ALA ILE VAL SEQRES 2 A 201 VAL ASP HIS GLY MET TYR LYS LYS TYR ASN GLN ASN SER SEQRES 3 A 201 ASP LYS ILE LYS VAL ARG VAL HIS GLN MET VAL ASN HIS SEQRES 4 A 201 ILE ASN GLU MET TYR ARG PRO LEU ASN ILE ALA ILE SER SEQRES 5 A 201 LEU ASN ARG LEU GLN ILE TRP SER LYS LYS ASP LEU ILE SEQRES 6 A 201 THR VAL LYS SER ALA SER ASN VAL THR LEU GLU SER PHE SEQRES 7 A 201 GLY ASN TRP ARG GLU THR VAL LEU LEU LYS GLN GLN ASN SEQRES 8 A 201 ASN ASP CYS ALA HIS LEU LEU THR ALA THR ASN LEU ASN SEQRES 9 A 201 ASP ASN THR ILE GLY LEU ALA TYR LYS LYS GLY MET CYS SEQRES 10 A 201 ASN PRO LYS LEU SER VAL GLY LEU VAL GLN ASP TYR SER SEQRES 11 A 201 PRO ASN VAL PHE MET VAL ALA VAL THR MET THR HIS GLU SEQRES 12 A 201 LEU GLY HIS ASN LEU GLY MET GLU HIS ASP ASP LYS ASP SEQRES 13 A 201 LYS CYS LYS CYS GLU ALA CYS ILE MET SER ASP VAL ILE SEQRES 14 A 201 SER ASP LYS PRO SER LYS LEU PHE SER ASP CYS SER LYS SEQRES 15 A 201 ASN ASP TYR GLN THR PHE LEU THR LYS TYR ASN PRO GLN SEQRES 16 A 201 CYS ILE LEU ASN ALA PRO HET ZN A 999 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *78(H2 O) HELIX 1 1 ASP A 15 TYR A 22 1 8 HELIX 2 2 ASN A 25 ARG A 45 1 21 HELIX 3 3 ALA A 70 VAL A 85 1 16 HELIX 4 4 VAL A 85 GLN A 90 1 6 HELIX 5 5 LEU A 103 THR A 107 5 5 HELIX 6 6 ASN A 132 LEU A 148 1 17 HELIX 7 7 ASP A 154 LYS A 159 1 6 HELIX 8 8 SER A 178 ASN A 193 1 16 HELIX 9 9 PRO A 194 LEU A 198 5 5 SHEET 1 A 5 ILE A 49 ILE A 58 0 SHEET 2 A 5 ARG A 6 VAL A 14 1 N LEU A 10 O SER A 52 SHEET 3 A 5 CYS A 94 THR A 99 1 O LEU A 98 N VAL A 13 SHEET 4 A 5 VAL A 123 GLN A 127 1 O GLY A 124 N LEU A 97 SHEET 5 A 5 GLY A 109 ALA A 111 -1 N LEU A 110 O LEU A 125 SSBOND 1 CYS A 117 CYS A 196 1555 1555 2.00 SSBOND 2 CYS A 158 CYS A 180 1555 1555 2.03 SSBOND 3 CYS A 160 CYS A 163 1555 1555 2.01 LINK ZN ZN A 999 NE2 HIS A 142 1555 1555 2.39 LINK ZN ZN A 999 NE2 HIS A 146 1555 1555 2.26 LINK ZN ZN A 999 NE2 HIS A 152 1555 1555 2.19 LINK ZN ZN A 999 O HOH A1011 1555 1555 2.44 SITE 1 AC1 4 HIS A 142 HIS A 146 HIS A 152 HOH A1011 CRYST1 77.800 77.800 82.300 90.00 90.00 90.00 P 43 21 2 8 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 0.012853 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012151 0.00000