HEADER HYDROLASE 05-MAY-05 1ZLB TITLE CRYSTAL STRUCTURE OF CATALYTICALLY-ACTIVE PHOSPHOLIPASE A2 IN THE TITLE 2 ABSENCE OF CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTENSIVE PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; 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 KEYWDS ASP49-PLA2, TOXIN, SNAKE VENOM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.T.MURAKAMI,A.C.CINTRA,A.GABDOULKHAKOV,N.GENOV,C.BETZEL,R.K.ARNI REVDAT 4 11-OCT-17 1ZLB 1 REMARK REVDAT 3 24-FEB-09 1ZLB 1 VERSN REVDAT 2 04-JUL-06 1ZLB 1 JRNL REVDAT 1 25-APR-06 1ZLB 0 JRNL AUTH M.T.MURAKAMI,A.GABDOULKHAKOV,N.GENOV,A.C.CINTRA,C.BETZEL, JRNL AUTH 2 R.K.ARNI JRNL TITL INSIGHTS INTO METAL ION BINDING IN PHOSPHOLIPASES A(2): JRNL TITL 2 ULTRA HIGH-RESOLUTION CRYSTAL STRUCTURES OF AN ACIDIC JRNL TITL 3 PHOSPHOLIPASE A(2) IN THE CA(2+) FREE AND BOUND STATES. JRNL REF BIOCHIMIE V. 88 543 2006 JRNL REFN ISSN 0300-9084 JRNL PMID 16376474 JRNL DOI 10.1016/J.BIOCHI.2005.10.014 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.T.MURAKAMI,S.MICHELAN-DUARTE,A.C.O.CINTRA,R.K.ARNI REMARK 1 TITL CRYSTALLIZATION AND HIGH-RESOLUTION X-RAY DIFFRACTION DATA REMARK 1 TITL 2 COLLECTION OF AN ASP49 PLA2 FROM BOTHROPS JARARACUSSU VENOM REMARK 1 TITL 3 BOTH IN THE PRESENCE AND ABSENCE OF CA2+ IONS. REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V.1703 79 2004 REMARK 1 REFN ISSN 0006-3002 REMARK 1 PMID 15588705 REMARK 1 DOI 10.1016/J.BBAPAP.2004.08.008 REMARK 2 REMARK 2 RESOLUTION. 0.97 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) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.151 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.168 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1731 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.141 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)) : 47269 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 950 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1160.4 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 810.20 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11031 REMARK 3 NUMBER OF RESTRAINTS : 13026 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.040 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.102 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.092 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.039 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.091 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZLB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032851. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.80 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57413 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06800 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) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 19.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NACL, EDTA, TRIS, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 44.90800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.90800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.98200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.89700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.98200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.89700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.90800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.98200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.89700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.90800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.98200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.89700 REMARK 290 SMTRY3 8 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 A 195 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 331 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 348 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 349 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 358 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 373 LIES ON A SPECIAL POSITION. 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 TYR A 11 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 TYR A 21 O - C - N ANGL. DEV. = -11.2 DEGREES REMARK 500 LEU A 22 C - N - CA ANGL. DEV. = -18.6 DEGREES REMARK 500 GLY A 29 C - N - CA ANGL. DEV. = 13.0 DEGREES REMARK 500 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 TYR A 51 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 TYR A 66 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 LYS A 68 C - N - CA ANGL. DEV. = 15.7 DEGREES REMARK 500 ASP A 72 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 VAL A 74 O - C - N ANGL. DEV. = -11.6 DEGREES REMARK 500 ARG A 90 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 22 SER A 23 146.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UMV RELATED DB: PDB REMARK 900 ISOFORM WITH BOUND CA2+ REMARK 900 RELATED ID: 1ZL7 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH BOUND CA2+ DBREF 1ZLB A 1 122 UNP Q8AXY1 Q8AXY1_BOTJR 17 138 SEQADV 1ZLB ASN A 58 UNP Q8AXY1 ASP 74 CONFLICT SEQADV 1ZLB ASN A 79 UNP Q8AXY1 ASP 95 CONFLICT 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 ASN 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 ASN 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 FORMUL 2 HOH *259(H2 O) HELIX 1 1 SER A 1 GLY A 14 1 14 HELIX 2 2 SER A 16 SER A 23 1 8 HELIX 3 3 ASP A 38 LYS A 53 1 16 HELIX 4 4 ASN A 79 ASN A 99 1 21 HELIX 5 5 LYS A 100 TYR A 103 5 4 HELIX 6 6 ASP A 104 TRP A 108 5 5 HELIX 7 7 GLY A 111 CYS A 115 5 5 SHEET 1 A 2 TYR A 66 LYS A 69 0 SHEET 2 A 2 ASP A 72 CYS A 75 -1 O VAL A 74 N SER A 67 SSBOND 1 CYS A 26 CYS A 115 1555 1555 2.03 SSBOND 2 CYS A 28 CYS A 44 1555 1555 2.02 SSBOND 3 CYS A 43 CYS A 95 1555 1555 2.04 SSBOND 4 CYS A 49 CYS A 122 1555 1555 2.03 SSBOND 5 CYS A 50 CYS A 88 1555 1555 2.03 SSBOND 6 CYS A 57 CYS A 81 1555 1555 2.02 SSBOND 7 CYS A 75 CYS A 86 1555 1555 2.03 CRYST1 39.964 53.794 89.816 90.00 90.00 90.00 C 2 2 21 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 0.025023 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011134 0.00000