10 20 30 40 50 60 70 80 1OXL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 02-APR-03 1OXL
TITLE INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL- TITLE 2 5-PROPYL-OCTAHYDRO-INDOL-7-YL)-ACETIC ACID (INDOLE): TITLE 3 CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PLA2 FROM TITLE 4 RUSSELL'S VIPER AND INDOLE AT 1.8 RESOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2 VRV-PL-VIIIA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE; COMPND 5 EC: 3.1.1.4
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DABOIA RUSSELLII RUSSELLII; SOURCE 3 ORGANISM_TAXID: 31159; SOURCE 4 STRAIN: RUSSELLII; SOURCE 5 SECRETION: VENOM
KEYWDS PHOSPHOLIPASE A2, INDOLE DERIVATIVE, INHIBITION, CRYSTAL KEYWDS 2 STRUCTURE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.CHANDRA,R.BALASUBRAMANYA,P.KAUR,T.P.SINGH
REVDAT 2 24-FEB-09 1OXL 1 VERSN REVDAT 1 06-APR-04 1OXL 0
JRNL AUTH R.BALASUBRAMANYA,V.CHANDRA,P.KAUR,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX OF THE SECRETORY JRNL TITL 2 PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA JRNL TITL 3 WITH AN ENDOGENIC INDOLE DERIVATIVE, JRNL TITL 4 2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL- JRNL TITL 5 ACETIC ACID AT 1.8 A RESOLUTION. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1752 177 2005 JRNL REFN ISSN 0006-3002 JRNL PMID 16122995 JRNL DOI 10.1016/J.BBAPAP.2005.07.020
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.CHANDRA,P.KAUR,J.JASTI,CH.BETZEL,T.P.SINGH REMARK 1 TITL REGULATION OF CATALYTIC FUNCTION BY MOLECULAR REMARK 1 TITL 2 ASSOCIATION: CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 REMARK 1 TITL 3 FROM DABOIA RUSSELLI PULCHELLA (DPLA2) AT 1.9 REMARK 1 TITL 4 RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 1793 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444901014524 REMARK 1 REFERENCE 2 REMARK 1 AUTH V.CHANDRA,P.KAUR,A.SRINIVASAN,T.P.SINGH REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF A PRESYNAPTIC REMARK 1 TITL 2 NEUROTOXIC PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI REMARK 1 TITL 3 PULCHELLA AT 2.4 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 296 1117 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.2000.3537
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21615 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) : 0.188 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1166 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1539 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1887 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 284 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.86000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 1.27000 REMARK 3 B12 (A**2) : 0.00000 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): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.697 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1964 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1665 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2630 ; 1.861 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3931 ; 1.047 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 232 ; 3.694 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 364 ;18.185 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 268 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2104 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 389 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 509 ; 0.352 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1581 ; 0.217 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 224 ; 0.186 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.016 ; 0.500 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): 17 ; 0.216 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.214 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.239 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): 2 ; 0.202 ; 0.500 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): 1195 ; 0.747 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1885 ; 1.404 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 769 ; 1.948 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 745 ; 3.141 ; 4.500 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 : BABINET MODEL WITH 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 1OXL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-03. REMARK 100 THE RCSB ID CODE IS RCSB018776.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.0 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 : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 21615 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.08300 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FB2 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 AMMONIUM SULPHATE BUFFER WITH REMARK 280 20MM SODIUM CACODYLATE, 50MM CALCIUM CHLORIDE, 3% DIOXANE, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
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 39.05300 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 39.05300 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 38.01000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.22100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.01000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.22100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.05300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.01000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.22100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.05300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.01000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.22100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 76.02000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 39.05300 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 38.01000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 44.22100 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -39.05300 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 38.01000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 44.22100 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 78.10600 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 38.01000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 44.22100 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 78.10600 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 38.01000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 44.22100 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -39.05300
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 B 542 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 GLY A 14 C LYS A 16 N 0.209 REMARK 500 PRO A 60 C LYS A 69 N 0.162 REMARK 500 LYS A 86 C GLY A 88 N 0.144 REMARK 500 ASP A 122 C PHE A 124 N 0.376 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 GLY A 14 O - C - N ANGL. DEV. = -10.3 DEGREES REMARK 500 LYS A 86 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 LYS A 86 O - C - N ANGL. DEV. = -22.9 DEGREES REMARK 500 GLY A 88 C - N - CA ANGL. DEV. = 20.3 DEGREES REMARK 500 ASP A 122 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 PRO B 60 O - C - N ANGL. DEV. = -12.3 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 LEU A 2 -34.59 -38.56 REMARK 500 SER A 24 24.43 -144.64 REMARK 500 ASP A 39 -172.60 -170.16 REMARK 500 LEU A 55 56.36 -119.32 REMARK 500 GLU A 85 -150.76 -51.65 REMARK 500 SER B 24 19.31 -140.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 14 11.78 REMARK 500 LYS A 86 -21.04 REMARK 500 GLY B 14 -11.29 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 A 581 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH A 593 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH A 594 DISTANCE = 6.13 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 B 301 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 B 302 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 401 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IDA A 501
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CL5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI REMARK 900 PULCHELLA REMARK 900 RELATED ID: 1FB2 RELATED DB: PDB REMARK 900 MUTANT (E219G) MALTOTETRAOSE-FORMING EXO-AMYLASE IN COMPLEX REMARK 900 WITH MALTOTETRAOSE
DBREF 1OXL A 1 121 UNP P59071 PA28_DABRP 1 121 DBREF 1OXL B 1 121 UNP P59071 PA28_DABRP 1 121
SEQRES 1 A 121 SER LEU LEU GLU PHE GLY LYS MET ILE LEU GLU GLU THR SEQRES 2 A 121 GLY LYS LEU ALA ILE PRO SER TYR SER SER TYR GLY CYS SEQRES 3 A 121 TYR CYS GLY TRP GLY GLY LYS GLY THR PRO LYS ASP ALA SEQRES 4 A 121 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 A 121 ASN LEU PRO ASP CYS ASN PRO LYS SER ASP ARG TYR LYS SEQRES 6 A 121 TYR LYS ARG VAL ASN GLY ALA ILE VAL CYS GLU LYS GLY SEQRES 7 A 121 THR SER CYS GLU ASN ARG ILE CYS GLU CYS ASP LYS ALA SEQRES 8 A 121 ALA ALA ILE CYS PHE ARG GLN ASN LEU ASN THR TYR SER SEQRES 9 A 121 LYS LYS TYR MET LEU TYR PRO ASP PHE LEU CYS LYS GLY SEQRES 10 A 121 GLU LEU LYS CYS SEQRES 1 B 121 SER LEU LEU GLU PHE GLY LYS MET ILE LEU GLU GLU THR SEQRES 2 B 121 GLY LYS LEU ALA ILE PRO SER TYR SER SER TYR GLY CYS SEQRES 3 B 121 TYR CYS GLY TRP GLY GLY LYS GLY THR PRO LYS ASP ALA SEQRES 4 B 121 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 B 121 ASN LEU PRO ASP CYS ASN PRO LYS SER ASP ARG TYR LYS SEQRES 6 B 121 TYR LYS ARG VAL ASN GLY ALA ILE VAL CYS GLU LYS GLY SEQRES 7 B 121 THR SER CYS GLU ASN ARG ILE CYS GLU CYS ASP LYS ALA SEQRES 8 B 121 ALA ALA ILE CYS PHE ARG GLN ASN LEU ASN THR TYR SER SEQRES 9 B 121 LYS LYS TYR MET LEU TYR PRO ASP PHE LEU CYS LYS GLY SEQRES 10 B 121 GLU LEU LYS CYS
HET CO3 B 301 4 HET CO3 B 302 4 HET SO4 B 401 5 HET IDA A 501 20
HETNAM CO3 CARBONATE ION HETNAM SO4 SULFATE ION HETNAM IDA (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL) HETNAM 2 IDA ACETIC ACID
FORMUL 3 CO3 2(C O3 2-) FORMUL 5 SO4 O4 S 2- FORMUL 6 IDA C15 H18 N2 O3 FORMUL 7 HOH *284(H2 O)
HELIX 1 1 SER A 1 GLY A 14 1 14 HELIX 2 2 LEU A 17 TYR A 22 1 6 HELIX 3 3 ASP A 39 ASN A 54 1 16 HELIX 4 4 THR A 89 ASN A 109 1 21 HELIX 5 5 LEU A 110 TYR A 113 5 4 HELIX 6 6 SER A 114 MET A 118 5 5 HELIX 7 7 PRO A 121 CYS A 126 5 5 HELIX 8 8 SER B 1 GLY B 14 1 14 HELIX 9 9 LEU B 17 TYR B 22 1 6 HELIX 10 10 ASP B 39 ASN B 54 1 16 HELIX 11 11 THR B 89 ASN B 109 1 21 HELIX 12 12 LEU B 110 TYR B 113 5 4 HELIX 13 13 SER B 114 MET B 118 5 5 HELIX 14 14 PRO B 121 CYS B 126 5 5
SHEET 1 A 2 TYR A 75 VAL A 78 0 SHEET 2 A 2 ALA A 81 CYS A 84 -1 O VAL A 83 N LYS A 76 SHEET 1 B 2 TYR B 75 VAL B 78 0 SHEET 2 B 2 ALA B 81 CYS B 84 -1 O VAL B 83 N LYS B 76
SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.03 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.02 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.04 SSBOND 4 CYS A 50 CYS A 132 1555 1555 2.02 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.01 SSBOND 6 CYS A 58 CYS A 91 1555 1555 2.04 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.04 SSBOND 8 CYS B 27 CYS B 126 1555 1555 2.02 SSBOND 9 CYS B 29 CYS B 45 1555 1555 2.04 SSBOND 10 CYS B 44 CYS B 105 1555 1555 2.03 SSBOND 11 CYS B 50 CYS B 132 1555 1555 2.03 SSBOND 12 CYS B 51 CYS B 98 1555 1555 2.05 SSBOND 13 CYS B 58 CYS B 91 1555 1555 2.01 SSBOND 14 CYS B 84 CYS B 96 1555 1555 2.04
CISPEP 1 ILE A 19 PRO A 20 0 10.02 CISPEP 2 ILE B 19 PRO B 20 0 4.57
SITE 1 AC1 4 PHE A 124 ARG B 107 GLN B 108 HOH B 443 SITE 1 AC2 3 ARG B 43 HOH B 416 HOH B 470 SITE 1 AC3 6 ARG A 77 SER B 114 LYS B 115 LYS B 116 SITE 2 AC3 6 HOH B 458 HOH B 555 SITE 1 AC4 12 LEU A 2 PHE A 5 GLY A 30 TRP A 31 SITE 2 AC4 12 HIS A 48 ASP A 49 TYR A 52 HOH A 518 SITE 3 AC4 12 HOH A 614 HOH A 615 HOH A 616 HOH A 619
CRYST1 76.020 88.442 78.106 90.00 90.00 90.00 C 2 2 21 16
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 0.013154 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011307 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012803 0.00000