PDB Short entry for 2PH4 HEADER TOXIN 10-APR-07 2PH4 TITLE CRYSTAL STRUCTURE OF A NOVEL ARG49 PHOSPHOLIPASE A2 HOMOLOGUE FROM TITLE 2 ZHAOERMIA MANGSHANENSIS VENOM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZHAOERMIATOXIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHOLIPASE A2 HOMOLOG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZHAOERMIA MANGSHANENSIS; SOURCE 3 ORGANISM_TAXID: 242058; SOURCE 4 SECRETION: VENOM KEYWDS SNAKE VENOM, ARG49, PHOSPHOLIPASE A2, MYOTOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR M.T.MURAKAMI,U.KUCH,D.MEBS,R.K.ARNI REVDAT 5 30-AUG-23 2PH4 1 REMARK REVDAT 4 13-JUL-11 2PH4 1 VERSN REVDAT 3 24-FEB-09 2PH4 1 VERSN REVDAT 2 15-APR-08 2PH4 1 JRNL REVDAT 1 18-MAR-08 2PH4 0 JRNL AUTH M.T.MURAKAMI,U.KUCH,C.BETZEL,D.MEBS,R.K.ARNI JRNL TITL CRYSTAL STRUCTURE OF A NOVEL MYOTOXIC ARG49 PHOSPHOLIPASE JRNL TITL 2 A(2) HOMOLOG (ZHAOERMIATOXIN) FROM ZHAOERMIA MANGSHANENSIS JRNL TITL 3 SNAKE VENOM: INSIGHTS INTO ARG49 COORDINATION AND THE ROLE JRNL TITL 4 OF LYS122 IN THE POLARIZATION OF THE C-TERMINUS. JRNL REF TOXICON V. 51 723 2008 JRNL REFN ISSN 0041-0101 JRNL PMID 18295812 JRNL DOI 10.1016/J.TOXICON.2007.11.018 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15931 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1800 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1173 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 235 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : 0.98000 REMARK 3 B33 (A**2) : -1.47000 REMARK 3 B12 (A**2) : 0.49000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.250 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.229 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.840 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2030 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2727 ; 2.223 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 242 ;13.676 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;35.521 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;19.202 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.450 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1466 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1339 ; 0.245 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1404 ; 0.328 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 267 ; 0.223 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 93 ; 0.234 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.309 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1248 ; 1.127 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1948 ; 1.829 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 907 ; 3.068 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 778 ; 4.163 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2PH4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 1.427 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17731 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 23.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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: PDB ENTRY 1Y4L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POLYETHYLENE GLYCOL 8,000; AMMONIUM REMARK 280 SULFATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.31267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.62533 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.31267 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 62.62533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE DIMER FOUND IN THE REMARK 300 ASYMMETRIC UNIT. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -72.93300 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 OG SER B 1 OE1 GLU B 4 1.91 REMARK 500 OG SER A 1 OE1 GLU A 4 2.05 REMARK 500 NZ LYS B 132 O HOH B 432 2.06 REMARK 500 O HOH A 430 O HOH A 447 2.19 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 NZ LYS A 7 O HOH B 510 4455 2.07 REMARK 500 O HOH A 482 O HOH B 470 4455 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 B 44 CB CYS B 44 SG -0.123 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 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 LYS A 87 CD - CE - NZ ANGL. DEV. = 13.9 DEGREES REMARK 500 ARG B 43 CG - CD - NE ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG B 43 NE - CZ - NH2 ANGL. DEV. = -4.3 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 GLU A 86 124.08 -39.65 REMARK 500 GLU B 86 117.81 -167.18 REMARK 500 THR B 120 -32.88 -34.37 REMARK 500 LYS B 129 138.64 -38.04 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 ASN A 88 PRO A 90 -135.14 REMARK 500 GLY B 32 ARG B 33 -129.65 REMARK 500 ASN B 88 PRO B 90 -117.77 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 402 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE IS NUMBERED BASED ON THE BOVINE PANCREATIC REMARK 999 PHOSPHOLIPASE A2. SO, NOT SEQUENTIAL NUMBERS INDICATE REMARK 999 DELETIONS AND INSERTIONS REGIONS IN COMPARISON WITH BOVINE REMARK 999 PANCREATIC PLA2. DBREF 2PH4 A 1 133 UNP P84776 PA2H_ZHAMA 1 121 DBREF 2PH4 B 1 133 UNP P84776 PA2H_ZHAMA 1 121 SEQRES 1 A 121 SER LEU ILE GLU LEU THR LYS MET VAL PHE GLN GLU THR SEQRES 2 A 121 GLY LYS ASN PRO VAL THR TYR TYR THR LEU TYR GLY CYS SEQRES 3 A 121 ASN CYS GLY VAL GLY ARG ARG GLY LYS PRO LYS ASP ALA SEQRES 4 A 121 THR ASP ARG CYS CYS PHE VAL HIS ARG CYS CYS TYR LYS SEQRES 5 A 121 LYS LEU THR GLY CYS ASP PRO LYS LYS ASP ARG TYR SER SEQRES 6 A 121 TYR SER TRP GLU ASN LYS ALA ILE VAL CYS GLY GLU LYS SEQRES 7 A 121 ASN PRO CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 A 121 VAL ALA ILE CYS LEU ARG LYS ASN LEU GLY THR TYR ASP SEQRES 9 A 121 LYS ASN TYR ARG PHE THR MET LYS PHE LEU CYS ASP LYS SEQRES 10 A 121 PRO GLU LYS CYS SEQRES 1 B 121 SER LEU ILE GLU LEU THR LYS MET VAL PHE GLN GLU THR SEQRES 2 B 121 GLY LYS ASN PRO VAL THR TYR TYR THR LEU TYR GLY CYS SEQRES 3 B 121 ASN CYS GLY VAL GLY ARG ARG GLY LYS PRO LYS ASP ALA SEQRES 4 B 121 THR ASP ARG CYS CYS PHE VAL HIS ARG CYS CYS TYR LYS SEQRES 5 B 121 LYS LEU THR GLY CYS ASP PRO LYS LYS ASP ARG TYR SER SEQRES 6 B 121 TYR SER TRP GLU ASN LYS ALA ILE VAL CYS GLY GLU LYS SEQRES 7 B 121 ASN PRO CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 B 121 VAL ALA ILE CYS LEU ARG LYS ASN LEU GLY THR TYR ASP SEQRES 9 B 121 LYS ASN TYR ARG PHE THR MET LYS PHE LEU CYS ASP LYS SEQRES 10 B 121 PRO GLU LYS CYS HET SO4 A 301 5 HET SO4 A 302 5 HET PEG A 401 7 HET SO4 B 303 5 HET SO4 B 304 5 HET SO4 B 305 5 HET PEG B 402 7 HETNAM SO4 SULFATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 SO4 5(O4 S 2-) FORMUL 5 PEG 2(C4 H10 O3) FORMUL 10 HOH *235(H2 O) HELIX 1 1 SER A 1 GLY A 15 1 14 HELIX 2 2 ASN A 17 THR A 23 1 7 HELIX 3 3 ASP A 39 LEU A 58 1 17 HELIX 4 4 ASN A 88 LEU A 110 1 22 HELIX 5 5 GLY A 111 TYR A 113 5 3 HELIX 6 6 ASP A 114 PHE A 123 5 10 HELIX 7 7 SER B 1 GLY B 15 1 14 HELIX 8 8 ASN B 17 THR B 23 1 7 HELIX 9 9 ASP B 39 LYS B 57 1 16 HELIX 10 10 ASN B 88 ASN B 109 1 21 HELIX 11 11 LEU B 110 TYR B 113 5 4 HELIX 12 12 ASP B 114 PHE B 123 5 10 SHEET 1 A 2 SER A 76 GLU A 78 0 SHEET 2 A 2 ALA A 81 VAL A 83 -1 O VAL A 83 N SER A 76 SHEET 1 B 2 SER B 76 TRP B 77 0 SHEET 2 B 2 ILE B 82 VAL B 83 -1 O VAL B 83 N SER B 76 SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.02 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.02 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.02 SSBOND 4 CYS A 50 CYS A 133 1555 1555 2.04 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.02 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.03 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.01 SSBOND 8 CYS B 27 CYS B 126 1555 1555 1.99 SSBOND 9 CYS B 29 CYS B 45 1555 1555 1.98 SSBOND 10 CYS B 44 CYS B 105 1555 1555 2.07 SSBOND 11 CYS B 50 CYS B 133 1555 1555 2.00 SSBOND 12 CYS B 51 CYS B 98 1555 1555 1.99 SSBOND 13 CYS B 61 CYS B 91 1555 1555 1.99 SSBOND 14 CYS B 84 CYS B 96 1555 1555 2.03 SITE 1 AC1 6 GLY A 32 ARG A 34 ARG A 49 HOH A 474 SITE 2 AC1 6 HOH A 486 PHE B 119 SITE 1 AC2 2 ARG A 34 LYS A 53 SITE 1 AC3 3 ARG B 34 ARG B 49 HOH B 484 SITE 1 AC4 5 LYS A 69 TYR B 21 LYS B 115 ARG B 118 SITE 2 AC4 5 HOH B 458 SITE 1 AC5 5 LYS A 132 CYS A 133 HOH A 449 ARG B 34 SITE 2 AC5 5 LYS B 53 SITE 1 AC6 2 HOH A 424 HOH A 459 SITE 1 AC7 4 PRO B 18 TYR B 22 THR B 23 HOH B 491 CRYST1 72.933 72.933 93.938 90.00 90.00 120.00 P 64 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 0.013711 0.007916 0.000000 0.00000 SCALE2 0.000000 0.015832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010645 0.00000