HEADER TOXIN 05-AUG-02 1MC2 TITLE MONOMERIC LYS-49 PHOSPHOLIPASE A2 HOMOLOGUE PURIFIED FROM AG COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACUTOHAEMONLYSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOLIPASE A2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINAGKISTRODON ACUTUS; SOURCE 3 ORGANISM_COMMON: CHINESE MOCCASIN; SOURCE 4 ORGANISM_TAXID: 36307 KEYWDS YS49-PHOSPHOLIPASE A2, SNAKE VENOM, AGKISTRODON ACUTUS, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.LIU,Q.Q.HUANG,R.G.ZHANG,C.M.WEEKS,C.JELSCH,M.K.TENG,L.W.NIU REVDAT 5 14-FEB-18 1MC2 1 REMARK REVDAT 4 11-OCT-17 1MC2 1 REMARK REVDAT 3 24-FEB-09 1MC2 1 VERSN REVDAT 2 24-FEB-04 1MC2 1 JRNL REVDAT 1 21-AUG-02 1MC2 0 JRNL AUTH Q.LIU,Q.Q.HUANG,M.K.TENG,C.M.WEEKS,C.JELSCH,R.G.ZHANG, JRNL AUTH 2 L.W.NIU JRNL TITL THE CRYSTAL STRUCTURE OF A NOVEL, INACTIVE, LYSINE 49 PLA2 JRNL TITL 2 FROM AGKISTRODON ACUTUS VENOM: AN ULTRAHIGH RESOLUTION, AB JRNL TITL 3 INITIO STRUCTURE DETERMINATION JRNL REF J.BIOL.CHEM. V. 278 41400 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12871974 JRNL DOI 10.1074/JBC.M305210200 REMARK 2 REMARK 2 RESOLUTION. 0.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.104 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.095 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.121 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3360 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 73203 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.095 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 62357 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 975 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 228 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1210.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 945.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11281 REMARK 3 NUMBER OF RESTRAINTS : 13526 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 ANGLE DISTANCES (A) : 0.034 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.109 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.155 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.131 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.036 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.083 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 5.12% (INCLUDE ALL DATA) REMARK 4 REMARK 4 1MC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90 REMARK 200 MONOCHROMATOR : MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73203 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : 0.02700 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 30.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.332 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 15.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, PH 5.8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 X+1/2,Y+1/2,Z 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 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 22.36600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.54300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.36600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.54300 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2004 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2044 LIES ON A SPECIAL POSITION. 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A1134 C CYS A1134 O -0.233 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 VAL A1018 CG1 - CB - CG2 ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG A1034 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A1043 CD - NE - CZ ANGL. DEV. = 47.0 DEGREES REMARK 500 ARG A1043 NH1 - CZ - NH2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A1043 NH1 - CZ - NH2 ANGL. DEV. = -9.2 DEGREES REMARK 500 ARG A1043 NE - CZ - NH1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A1043 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A1043 NE - CZ - NH2 ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG A1107 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 LYS A1122 CA - CB - CG ANGL. DEV. = -14.6 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 LEU A1024 20.06 -144.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 1135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 1136 DBREF 1MC2 A 1001 1134 UNP O57385 PA2H_AGKAC 17 138 SEQRES 1 A 122 SER LEU PHE GLU LEU GLY LYS MET ILE TRP GLN GLU THR SEQRES 2 A 122 GLY LYS ASN PRO VAL LYS ASN TYR GLY LEU TYR GLY CYS SEQRES 3 A 122 ASN CYS GLY VAL GLY GLY ARG GLY GLU PRO LEU ASP ALA SEQRES 4 A 122 THR ASP ARG CYS CYS PHE VAL HIS LYS CYS CYS TYR LYS SEQRES 5 A 122 LYS LEU THR ASP CYS ASP SER LYS LYS ASP ARG TYR SER SEQRES 6 A 122 TYR LYS TRP LYS ASN LYS ALA ILE VAL CYS GLY LYS ASN SEQRES 7 A 122 GLN PRO CYS MET GLN GLU MET CYS GLU CYS ASP LYS ALA SEQRES 8 A 122 PHE ALA ILE CYS LEU ARG GLU ASN LEU ASP THR TYR ASN SEQRES 9 A 122 LYS SER PHE ARG TYR HIS LEU LYS PRO SER CYS LYS LYS SEQRES 10 A 122 THR SER GLU GLN CYS HET IPA A1135 4 HET IPA A1136 4 HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 2 IPA 2(C3 H8 O) FORMUL 4 HOH *228(H2 O) HELIX 1 1 SER A 1001 GLY A 1014 1 14 HELIX 2 2 ASN A 1016 GLY A 1023 1 7 HELIX 3 3 ASP A 1039 LYS A 1053 1 15 HELIX 4 4 GLN A 1089 ASN A 1109 1 21 HELIX 5 5 LEU A 1110 TYR A 1113 5 4 HELIX 6 6 ASN A 1114 ARG A 1118 5 5 HELIX 7 7 LEU A 1121 CYS A 1125 5 5 SHEET 1 A 2 TYR A1075 LYS A1078 0 SHEET 2 A 2 ALA A1081 CYS A1084 -1 O VAL A1083 N LYS A1076 SSBOND 1 CYS A 1027 CYS A 1125 1555 1555 2.06 SSBOND 2 CYS A 1029 CYS A 1045 1555 1555 2.03 SSBOND 3 CYS A 1044 CYS A 1105 1555 1555 2.04 SSBOND 4 CYS A 1050 CYS A 1134 1555 1555 2.07 SSBOND 5 CYS A 1051 CYS A 1098 1555 1555 2.05 SSBOND 6 CYS A 1061 CYS A 1091 1555 1555 2.05 SSBOND 7 CYS A 1084 CYS A 1096 1555 1555 2.04 SITE 1 AC1 4 PRO A1017 HOH A2032 HOH A2104 HOH A2204 SITE 1 AC2 4 GLY A1006 VAL A1018 TYR A1119 HOH A2075 CRYST1 44.732 59.086 45.308 90.00 117.43 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 0.022355 0.000000 0.011603 0.00000 SCALE2 0.000000 0.016924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024867 0.00000