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 <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) : 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
