HEADER HYDROLASE 02-AUG-04 1U73 TITLE CRYSTAL STRUCTURE OF A DIMERIC ACIDIC PLATELET AGGREGATION INHIBITOR TITLE 2 AND HYPOTENSIVE PHOSPHOLIPASE A2 FROM BOTHROPS JARARACUSSU COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTENSIVE PHOSPHOLIPASE A2; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOTHROPS JARARACUSSU; SOURCE 3 ORGANISM_COMMON: JARARACUSSU; SOURCE 4 ORGANISM_TAXID: 8726; SOURCE 5 OTHER_DETAILS: VENOM GLANDS KEYWDS ACIDIC PHOSPHOLIPASE A2, BOTHROPS JARARACUSSU VENOM, PLATELET KEYWDS 2 AGGREGATION AND HYPOTENSIVE EFFECTS, OLIGOMERIC STATE, DIMERIC, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.MAGRO,M.T.MURAKAMI,A.M.SOARES,R.K.ARNI,M.R.FONTES REVDAT 3 03-APR-24 1U73 1 REMARK REVDAT 2 24-FEB-09 1U73 1 VERSN REVDAT 1 12-OCT-04 1U73 0 JRNL AUTH A.J.MAGRO,M.T.MURAKAMI,S.MARCUSSI,A.M.SOARES,R.K.ARNI, JRNL AUTH 2 M.R.FONTES JRNL TITL CRYSTAL STRUCTURE OF AN ACIDIC PLATELET AGGREGATION JRNL TITL 2 INHIBITOR AND HYPOTENSIVE PHOSPHOLIPASE A(2) IN THE JRNL TITL 3 MONOMERIC AND DIMERIC STATES: INSIGHTS INTO ITS OLIGOMERIC JRNL TITL 4 STATE JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 323 24 2004 JRNL REFN ISSN 0006-291X JRNL PMID 15351695 JRNL DOI 10.1016/J.BBRC.2004.08.046 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.H.ANDRIAO-ESCARSO,A.M.SOARES,M.R.FONTES,A.L.FULY, REMARK 1 AUTH 2 F.M.CORREA,J.C.ROSA,L.J.GREENE,J.R.GIGLIO REMARK 1 TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF AN ACIDIC REMARK 1 TITL 2 PLATELET AGGREGATION INHIBITOR AND HYPOTENSIVE PHOSPHOLIPASE REMARK 1 TITL 3 A2 FROM BOTHROPS JARARACUSSU VENOM REMARK 1 REF BIOCHEM.PHARM. V. 64 723 2002 REMARK 1 REFN ISSN 0006-2952 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.70 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) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 14151 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) : 0.190 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 712 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 : 1900 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 381 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.19000 REMARK 3 B22 (A**2) : -3.11000 REMARK 3 B33 (A**2) : 4.29000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.40000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 4.00 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) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1U73 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.38 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS 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 : 14151 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.29300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.000 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: BTHA-I (MONOMERIC FORM) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG 6000, PH 3.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 31.56800 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP B 42 O HOH B 183 2.08 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 SER A 24 87.07 -150.46 REMARK 500 ASP B 39 -165.37 -165.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UMV RELATED DB: PDB REMARK 900 MONOMERIC ACIDIC PHOSPHOLIPASE A2 FROM BOTHROPS JARARACUSSU DBREF 1U73 A 1 133 UNP Q8AXY1 Q8AXY1_BOTJR 17 138 DBREF 1U73 B 1 133 UNP Q8AXY1 Q8AXY1_BOTJR 17 138 SEQRES 1 A 122 SER LEU TRP GLN PHE GLY LYS MET ILE ASN TYR VAL MET SEQRES 2 A 122 GLY GLU SER GLY VAL LEU GLN TYR LEU SER TYR GLY CYS SEQRES 3 A 122 TYR CYS GLY LEU GLY GLY GLN GLY GLN PRO THR ASP ALA SEQRES 4 A 122 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 A 122 LYS VAL THR GLY CYS ASP PRO LYS ILE ASP SER TYR THR SEQRES 6 A 122 TYR SER LYS LYS ASN GLY ASP VAL VAL CYS GLY GLY ASP SEQRES 7 A 122 ASP PRO CYS LYS LYS GLN ILE CYS GLU CYS ASP ARG VAL SEQRES 8 A 122 ALA THR THR CYS PHE ARG ASP ASN LYS ASP THR TYR ASP SEQRES 9 A 122 ILE LYS TYR TRP PHE TYR GLY ALA LYS ASN CYS GLN GLU SEQRES 10 A 122 LYS SER GLU PRO CYS SEQRES 1 B 122 SER LEU TRP GLN PHE GLY LYS MET ILE ASN TYR VAL MET SEQRES 2 B 122 GLY GLU SER GLY VAL LEU GLN TYR LEU SER TYR GLY CYS SEQRES 3 B 122 TYR CYS GLY LEU GLY GLY GLN GLY GLN PRO THR ASP ALA SEQRES 4 B 122 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 B 122 LYS VAL THR GLY CYS ASP PRO LYS ILE ASP SER TYR THR SEQRES 6 B 122 TYR SER LYS LYS ASN GLY ASP VAL VAL CYS GLY GLY ASP SEQRES 7 B 122 ASP PRO CYS LYS LYS GLN ILE CYS GLU CYS ASP ARG VAL SEQRES 8 B 122 ALA THR THR CYS PHE ARG ASP ASN LYS ASP THR TYR ASP SEQRES 9 B 122 ILE LYS TYR TRP PHE TYR GLY ALA LYS ASN CYS GLN GLU SEQRES 10 B 122 LYS SER GLU PRO CYS FORMUL 3 HOH *381(H2 O) HELIX 1 1 SER A 1 GLY A 15 1 14 HELIX 2 2 SER A 17 LEU A 23 1 7 HELIX 3 3 ASP A 39 GLY A 53 1 15 HELIX 4 4 ASP A 88 ASN A 109 1 21 HELIX 5 5 LYS A 110 TYR A 113 5 4 HELIX 6 6 ASP A 114 TRP A 118 5 5 HELIX 7 7 GLY A 121 GLN A 127 5 6 HELIX 8 8 SER B 1 GLY B 15 1 14 HELIX 9 9 SER B 17 LEU B 23 1 7 HELIX 10 10 ASP B 39 LYS B 57 1 16 HELIX 11 11 ASP B 88 ASN B 109 1 21 HELIX 12 12 LYS B 110 TYR B 113 5 4 HELIX 13 13 ASP B 114 TRP B 118 5 5 HELIX 14 14 GLY B 121 GLN B 127 5 6 SHEET 1 A 2 TYR A 75 LYS A 78 0 SHEET 2 A 2 ASP A 81 CYS A 84 -1 O VAL A 83 N SER A 76 SHEET 1 B 2 THR B 74 LYS B 78 0 SHEET 2 B 2 ASP B 81 GLY B 85 -1 O ASP B 81 N LYS B 78 SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.03 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.03 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.03 SSBOND 4 CYS A 50 CYS A 133 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.03 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.04 SSBOND 8 CYS B 27 CYS B 126 1555 1555 2.03 SSBOND 9 CYS B 29 CYS B 45 1555 1555 2.03 SSBOND 10 CYS B 44 CYS B 105 1555 1555 2.03 SSBOND 11 CYS B 50 CYS B 133 1555 1555 2.03 SSBOND 12 CYS B 51 CYS B 98 1555 1555 2.03 SSBOND 13 CYS B 61 CYS B 91 1555 1555 2.03 SSBOND 14 CYS B 84 CYS B 96 1555 1555 2.04 CRYST1 33.193 63.136 47.407 90.00 102.30 90.00 P 1 21 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 0.030127 0.000000 0.006569 0.00000 SCALE2 0.000000 0.015839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021590 0.00000