PDB Short entry for 2WQ5 HEADER HYDROLASE 13-AUG-09 2WQ5 TITLE NON-ANTIBIOTIC PROPERTIES OF TETRACYCLINES: STRUCTURAL BASIS FOR TITLE 2 INHIBITION OF SECRETORY PHOSPHOLIPASE A2. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2, ACIDIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOLIPASE A2, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE; COMPND 5 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA NAJA; SOURCE 3 ORGANISM_COMMON: INDIAN COBRA; SOURCE 4 ORGANISM_TAXID: 35670; SOURCE 5 ORGAN: VENOM SACK KEYWDS HYDROLASE, MINOCYCLINE, PHOSPHOLIPASE, METAL-BINDING, LIPID KEYWDS 2 DEGRADATION, CALCIUM BINDING LOOP, CARBOXYLIC ESTER HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.DALM,G.J.PALM,W.HINRICHS REVDAT 5 20-DEC-23 2WQ5 1 COMPND REMARK HETNAM LINK REVDAT 4 28-JUN-17 2WQ5 1 REMARK REVDAT 3 13-JUL-11 2WQ5 1 VERSN REVDAT 2 14-APR-10 2WQ5 1 JRNL REVDAT 1 23-MAR-10 2WQ5 0 JRNL AUTH D.DALM,G.J.PALM,A.ALEKSANDROV,T.SIMONSON,W.HINRICHS JRNL TITL NON-ANTIBIOTIC PROPERTIES OF TETRACYCLINES: STRUCTURAL BASIS JRNL TITL 2 FOR INHIBITION OF SECRETORY PHOSPHOLIPASE A(2). JRNL REF J.MOL.BIOL. V. 398 83 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20211188 JRNL DOI 10.1016/J.JMB.2010.02.049 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 12547 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 + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 638 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 899 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 925 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 167 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 23.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.78 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.120 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.895 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1012 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 677 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1387 ; 1.459 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1617 ; 0.905 ; 3.017 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 122 ; 6.749 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;37.667 ;24.375 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 149 ;13.963 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;12.062 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 136 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1151 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 216 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 269 ; 0.257 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 759 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 525 ; 0.194 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 498 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 96 ; 0.169 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.020 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 27 ; 0.298 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 49 ; 0.205 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.260 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.018 ; 0.200 REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 615 ; 0.806 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 250 ; 0.243 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 961 ; 1.264 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 471 ; 1.837 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 426 ; 2.517 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 15 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1928 5.3930 23.5886 REMARK 3 T TENSOR REMARK 3 T11: 0.0135 T22: 0.0249 REMARK 3 T33: -0.0346 T12: -0.0170 REMARK 3 T13: 0.0125 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 6.1026 L22: 2.0124 REMARK 3 L33: 3.2676 L12: -0.5902 REMARK 3 L13: -0.9836 L23: 0.3638 REMARK 3 S TENSOR REMARK 3 S11: 0.1271 S12: -0.2161 S13: 0.2636 REMARK 3 S21: 0.0420 S22: -0.0248 S23: -0.0981 REMARK 3 S31: -0.0703 S32: 0.2953 S33: -0.1023 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 16 A 26 REMARK 3 ORIGIN FOR THE GROUP (A): -4.9818 12.7922 16.3823 REMARK 3 T TENSOR REMARK 3 T11: 0.1691 T22: 0.0194 REMARK 3 T33: 0.0042 T12: 0.0499 REMARK 3 T13: 0.0941 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.7659 L22: 2.7678 REMARK 3 L33: 8.3622 L12: 0.8689 REMARK 3 L13: -2.5220 L23: -2.5416 REMARK 3 S TENSOR REMARK 3 S11: 0.2596 S12: -0.1049 S13: 0.3173 REMARK 3 S21: 0.7639 S22: 0.0974 S23: 0.2581 REMARK 3 S31: -0.8587 S32: 0.0030 S33: -0.3571 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 27 A 32 REMARK 3 ORIGIN FOR THE GROUP (A): -12.1994 11.3635 8.0170 REMARK 3 T TENSOR REMARK 3 T11: 0.0376 T22: 0.0728 REMARK 3 T33: 0.0990 T12: 0.0596 REMARK 3 T13: 0.0717 T23: 0.0766 REMARK 3 L TENSOR REMARK 3 L11: 12.2709 L22: 5.7049 REMARK 3 L33: 17.4201 L12: 5.9341 REMARK 3 L13: 5.8514 L23: 5.3526 REMARK 3 S TENSOR REMARK 3 S11: 0.2052 S12: -0.1738 S13: 0.4386 REMARK 3 S21: -0.3373 S22: 0.2368 S23: 0.8938 REMARK 3 S31: -1.0169 S32: -1.1283 S33: -0.4420 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 33 A 53 REMARK 3 ORIGIN FOR THE GROUP (A): -10.1406 4.6317 6.7527 REMARK 3 T TENSOR REMARK 3 T11: 0.0357 T22: 0.0628 REMARK 3 T33: 0.0103 T12: 0.0078 REMARK 3 T13: -0.0081 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 4.1506 L22: 1.2356 REMARK 3 L33: 2.1294 L12: 1.8306 REMARK 3 L13: -2.8725 L23: -1.1050 REMARK 3 S TENSOR REMARK 3 S11: -0.0706 S12: 0.4022 S13: 0.1280 REMARK 3 S21: -0.0919 S22: 0.0977 S23: 0.0506 REMARK 3 S31: -0.0003 S32: -0.2323 S33: -0.0270 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 54 A 83 REMARK 3 ORIGIN FOR THE GROUP (A): -17.4744 -1.9036 21.6970 REMARK 3 T TENSOR REMARK 3 T11: 0.0206 T22: -0.0274 REMARK 3 T33: -0.0079 T12: -0.0061 REMARK 3 T13: 0.0220 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 4.8498 L22: 1.2496 REMARK 3 L33: 2.6708 L12: -0.0666 REMARK 3 L13: 0.7708 L23: -0.3962 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: -0.2268 S13: -0.2742 REMARK 3 S21: 0.1132 S22: -0.0293 S23: 0.0514 REMARK 3 S31: 0.1577 S32: 0.0126 S33: 0.0004 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 84 A 119 REMARK 3 ORIGIN FOR THE GROUP (A): -7.1067 7.7377 11.2511 REMARK 3 T TENSOR REMARK 3 T11: 0.0147 T22: -0.0232 REMARK 3 T33: -0.0309 T12: 0.0255 REMARK 3 T13: 0.0149 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.7990 L22: 0.7792 REMARK 3 L33: 2.0502 L12: 0.4184 REMARK 3 L13: -1.1965 L23: -0.7839 REMARK 3 S TENSOR REMARK 3 S11: 0.1134 S12: 0.0229 S13: 0.0548 REMARK 3 S21: 0.0443 S22: -0.0535 S23: -0.0080 REMARK 3 S31: -0.1051 S32: 0.0527 S33: -0.0599 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2WQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1290040668. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL 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 : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13314 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 34.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1A3D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 4000, 0.24M (NH4)2SO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 34.35600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.35600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.35600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.35600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.35600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.35600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 34.35600 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 34.35600 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 34.35600 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 34.35600 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 34.35600 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 34.35600 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 34.35600 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 34.35600 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 34.35600 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 34.35600 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 34.35600 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 34.35600 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 -34.35600 REMARK 350 BIOMT2 2 0.000000 0.000000 -1.000000 34.35600 REMARK 350 BIOMT3 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 34.35600 REMARK 350 BIOMT3 3 0.000000 -1.000000 0.000000 34.35600 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 CA CA A1001 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2011 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2165 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2166 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 59 CD CE NZ 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 ASN A 111 O HOH A 2152 1.96 REMARK 500 O1 MIY A 1120 O HOH A 2167 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O ASN A 111 NZ LYS A 115 8555 2.15 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 ASP A 23 81.06 -158.17 REMARK 500 ARG A 30 -151.95 -155.91 REMARK 500 SER A 33 102.93 37.21 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 SER A 33 GLY A 34 140.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2006 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2008 DISTANCE = 5.89 ANGSTROMS 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 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 39 OD1 REMARK 620 2 ASP A 39 OD1 119.7 REMARK 620 3 ASP A 39 OD1 119.8 119.8 REMARK 620 4 ASP A 39 OD2 78.4 138.5 51.3 REMARK 620 5 ASP A 39 OD2 138.5 51.3 78.4 89.6 REMARK 620 6 ASP A 39 OD2 51.3 78.4 138.5 89.6 89.5 REMARK 620 7 HOH A2064 O 137.1 73.1 69.6 120.7 83.0 148.6 REMARK 620 8 HOH A2064 O 73.1 69.6 137.2 148.6 120.6 82.9 75.0 REMARK 620 9 HOH A2064 O 69.6 137.1 73.2 83.0 148.7 120.6 75.0 75.0 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MIY A 1120 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PSH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM INDIAN COBRA REVEALS A REMARK 900 TRIMERIC ASSOCIATION REMARK 900 RELATED ID: 1OWS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A C49 PHOSPHOLIPASE A2 FROM INDIANCOBRA REMARK 900 REVEALS CARBOHYDRATE BINDING IN THE HYDROPHOBICCHANNEL REMARK 900 RELATED ID: 1A3F RELATED DB: PDB REMARK 900 PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM REMARK 900 RELATED ID: 1A3D RELATED DB: PDB REMARK 900 PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN PURIFIED FROM NATURAL SOURCE. CONFLICTS BELOW ARE REMARK 999 REPORTED AS NATURAL VARIANTS BY THIS AUTHOR. DBREF 2WQ5 A 1 119 UNP P15445 PA2_NAJNA 1 119 SEQADV 2WQ5 LYS A 59 UNP P15445 GLY 59 CONFLICT SEQADV 2WQ5 PHE A 63 UNP P15445 TYR 63 CONFLICT SEQADV 2WQ5 LYS A 70 UNP P15445 GLU 70 CONFLICT SEQADV 2WQ5 GLY A 81 UNP P15445 ASP 81 CONFLICT SEQRES 1 A 119 ASN LEU TYR GLN PHE LYS ASN MET ILE LYS CYS THR VAL SEQRES 2 A 119 PRO SER ARG SER TRP TRP ASP PHE ALA ASP TYR GLY CYS SEQRES 3 A 119 TYR CYS GLY ARG GLY GLY SER GLY THR PRO VAL ASP ASP SEQRES 4 A 119 LEU ASP ARG CYS CYS GLN VAL HIS ASP ASN CYS TYR ASN SEQRES 5 A 119 GLU ALA GLU LYS ILE SER LYS CYS TRP PRO PHE PHE LYS SEQRES 6 A 119 THR TYR SER TYR LYS CYS SER GLN GLY THR LEU THR CYS SEQRES 7 A 119 LYS GLY GLY ASN ASN ALA CYS ALA ALA SER VAL CYS ASP SEQRES 8 A 119 CYS ASP ARG LEU ALA ALA ILE CYS PHE ALA GLY ALA PRO SEQRES 9 A 119 TYR ASN ASP ASN ASN TYR ASN ILE ASP LEU LYS ALA ARG SEQRES 10 A 119 CYS GLN HET CA A1001 1 HET SO4 A1002 5 HET MIY A1120 33 HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM MIY (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A- HETNAM 2 MIY TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A- HETNAM 3 MIY OCTAHYDROTETRACENE-2- CARBOXAMIDE HETSYN MIY MINOCYCLINE FORMUL 2 CA CA 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 MIY C23 H27 N3 O7 FORMUL 5 HOH *167(H2 O) HELIX 1 1 ASN A 1 VAL A 13 1 13 HELIX 2 2 SER A 17 ALA A 22 5 6 HELIX 3 3 ASP A 38 GLU A 55 1 18 HELIX 4 4 TRP A 61 LYS A 65 5 5 HELIX 5 5 ASN A 83 ALA A 103 1 21 HELIX 6 6 ASN A 106 ASN A 109 5 4 HELIX 7 7 ASP A 113 CYS A 118 1 6 SHEET 1 AA 2 TYR A 69 SER A 72 0 SHEET 2 AA 2 THR A 75 CYS A 78 -1 O THR A 75 N SER A 72 SSBOND 1 CYS A 11 CYS A 71 1555 1555 2.02 SSBOND 2 CYS A 26 CYS A 118 1555 1555 2.03 SSBOND 3 CYS A 28 CYS A 44 1555 1555 2.02 SSBOND 4 CYS A 43 CYS A 99 1555 1555 2.02 SSBOND 5 CYS A 50 CYS A 92 1555 1555 2.05 SSBOND 6 CYS A 60 CYS A 85 1555 1555 2.04 SSBOND 7 CYS A 78 CYS A 90 1555 1555 2.02 LINK OD1 ASP A 39 CA CA A1001 5555 1555 2.67 LINK OD1 ASP A 39 CA CA A1001 9555 1555 2.67 LINK OD1 ASP A 39 CA CA A1001 1555 1555 2.67 LINK OD2 ASP A 39 CA CA A1001 1555 1555 2.40 LINK OD2 ASP A 39 CA CA A1001 9555 1555 2.40 LINK OD2 ASP A 39 CA CA A1001 5555 1555 2.40 LINK CA CA A1001 O HOH A2064 1555 1555 2.74 LINK CA CA A1001 O HOH A2064 1555 9555 2.74 LINK CA CA A1001 O HOH A2064 1555 5555 2.74 SITE 1 AC1 2 ASP A 39 HOH A2064 SITE 1 AC2 8 GLN A 4 ASN A 7 TRP A 61 TYR A 69 SITE 2 AC2 8 HOH A2161 HOH A2162 HOH A2163 HOH A2164 SITE 1 AC3 10 LEU A 2 TYR A 3 TRP A 18 ALA A 22 SITE 2 AC3 10 GLY A 29 ARG A 30 PHE A 64 HOH A2165 SITE 3 AC3 10 HOH A2166 HOH A2167 CRYST1 68.712 68.712 68.712 90.00 90.00 90.00 P 21 3 12 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 0.014553 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014553 0.00000