HEADER TOXIN 30-JUN-99 1QUA TITLE CRYSTAL STRUCTURE OF ACUTOLYSIN-C, A HEMORRHAGIC TOXIN FROM THE SNAKE TITLE 2 VENOM OF AGKISTRODON ACUTUS, AT 2.2 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACUTOLYSIN-C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEMORRHAGIN III SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINAGKISTRODON ACUTUS; SOURCE 3 ORGANISM_COMMON: CHINESE MOCCASIN; SOURCE 4 ORGANISM_TAXID: 36307; SOURCE 5 SECRETION: VENOM KEYWDS METALLOPROTEASE, HEMORRHAGIC TOXIN, SNAKE VENOM PROTEINASE, KEYWDS 2 AGKISTRODON ACUTUS, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR L.NIU,M.TENG,X.ZHU REVDAT 5 03-APR-24 1QUA 1 REMARK REVDAT 4 27-DEC-23 1QUA 1 REMARK LINK REVDAT 3 04-APR-18 1QUA 1 REMARK REVDAT 2 24-FEB-09 1QUA 1 VERSN REVDAT 1 05-JUL-00 1QUA 0 JRNL AUTH X.ZHU,M.TENG,L.NIU JRNL TITL STRUCTURE OF ACUTOLYSIN-C, A HAEMORRHAGIC TOXIN FROM THE JRNL TITL 2 VENOM OF AGKISTRODON ACUTUS, PROVIDING FURTHER EVIDENCE FOR JRNL TITL 3 THE MECHANISM OF THE PH-DEPENDENT PROTEOLYTIC REACTION OF JRNL TITL 4 ZINC METALLOPROTEINASES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 1834 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10531480 JRNL DOI 10.1107/S0907444999010306 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.GONG,Z.ZHU,L.NIU,M.TENG REMARK 1 TITL PRELIMINARY X-RAY DIFFRACTION ANALYSIS OF HEMORRHAGIN III REMARK 1 TITL 2 FROM THE SNAKE VENOM OF AGKISTRODON ACUTUS REMARK 1 REF CHIN.SCI.BULL. V. 41 544 1996 REMARK 1 REFN ISSN 1001-6538 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) (%) : 84.3 REMARK 3 NUMBER OF REFLECTIONS : 9688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1029 REMARK 3 BIN R VALUE (WORKING SET) : 0.2225 REMARK 3 BIN FREE R VALUE : 0.2503 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 : 1497 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.84 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) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.850 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000001206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 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 : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08000 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26300 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: CRYSTAL STRUCTURE OF H2-PROTEINASE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 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 23.41900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.67150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.76200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.67150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.41900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.76200 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 ALA A 3 -42.83 -142.31 REMARK 500 ASP A 85 -70.91 -125.11 REMARK 500 CYS A 117 -19.63 86.92 REMARK 500 LEU A 197 59.06 -95.73 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 105.1 REMARK 620 3 HIS A 152 NE2 104.9 97.6 REMARK 620 4 HOH A 300 O 113.7 102.2 129.6 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 1QUA A 10 180 UNP Q9W7S2 Q9W7S2_AGKAC 201 372 SEQRES 1 A 197 PRO ALA PRO GLN THR SER ILE GLU LEU PHE LEU ILE VAL SEQRES 2 A 197 ASP HIS SER MET TYR ALA LYS TYR ASN SER ASN SER SER SEQRES 3 A 197 LYS ILE THR THR THR LEU LYS ALA ARG VAL ASN ILE MET SEQRES 4 A 197 ASN ALA ILE TYR SER SER LEU ASN LEU VAL ILE THR LEU SEQRES 5 A 197 SER GLY ILE GLU MET TRP SER ALA ALA ASP LEU ILE THR SEQRES 6 A 197 VAL GLN SER SER SER ARG ASN THR LEU LYS LEU PHE ALA SEQRES 7 A 197 SER TRP ARG GLU THR ASP LEU LEU LYS ARG THR SER ASN SEQRES 8 A 197 ASP ASN ALA GLN LEU LEU THR ALA THR ASN PHE ASN GLY SEQRES 9 A 197 ASN THR VAL GLY LEU ALA TYR LEU LYS THR MET CYS ASN SEQRES 10 A 197 SER LYS TYR SER VAL GLY LEU ILE GLN ASP HIS SER ALA SEQRES 11 A 197 ILE PRO LEU LEU MET ALA VAL THR MET ALA HIS GLU LEU SEQRES 12 A 197 GLY HIS ASN LEU GLY MET ASN HIS ASP GLY ALA GLY CYS SEQRES 13 A 197 SER CYS ALA THR CYS ILE MET ALA PRO VAL LEU SER SER SEQRES 14 A 197 GLY PRO ALA LYS SER PHE SER ASP CYS SER LYS HIS ASP SEQRES 15 A 197 TYR GLN SER PHE LEU THR ILE HIS LYS PRO GLN CYS LEU SEQRES 16 A 197 LEU ASN HET ZN A 999 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *105(H2 O) HELIX 1 1 HIS A 16 TYR A 22 1 7 HELIX 2 2 SER A 26 SER A 46 1 21 HELIX 3 3 SER A 71 ARG A 89 1 19 HELIX 4 4 PRO A 133 ASN A 147 1 15 HELIX 5 5 ASP A 178 HIS A 191 1 14 SHEET 1 A 5 GLY A 109 ALA A 111 0 SHEET 2 A 5 VAL A 123 GLN A 127 -1 N LEU A 125 O LEU A 110 SHEET 3 A 5 ASN A 94 THR A 99 1 N ALA A 95 O GLY A 124 SHEET 4 A 5 THR A 6 VAL A 14 1 N PHE A 11 O ASN A 94 SHEET 5 A 5 LEU A 49 MET A 58 1 N VAL A 50 O THR A 6 SSBOND 1 CYS A 117 CYS A 195 1555 1555 2.03 SSBOND 2 CYS A 157 CYS A 179 1555 1555 2.02 SSBOND 3 CYS A 159 CYS A 162 1555 1555 2.02 LINK NE2 HIS A 142 ZN ZN A 999 1555 1555 2.05 LINK NE2 HIS A 146 ZN ZN A 999 1555 1555 2.08 LINK NE2 HIS A 152 ZN ZN A 999 1555 1555 1.88 LINK O HOH A 300 ZN ZN A 999 1555 1555 1.98 SITE 1 AC1 4 HIS A 142 HIS A 146 HIS A 152 HOH A 300 CRYST1 46.838 49.524 95.343 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 0.021350 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020192 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010488 0.00000