HEADER HYDROLASE 06-FEB-07 2OSH TITLE CRYSTAL STRUCTURE OF NATRATOXIN, A SNAKE SPLA2 THAT BLOCKS A-TYPE K+ TITLE 2 CHANNEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE; COMPND 5 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA ATRA; SOURCE 3 ORGANISM_COMMON: CHINESE COBRA; SOURCE 4 ORGANISM_TAXID: 8656; SOURCE 5 SECRETION: VENOM KEYWDS NAJA ATRA VENOM, PHOSPHOLIPASE A2, A-TYPE K+ CHANNEL INHIBITOR, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.TENG,L.SUN REVDAT 5 25-OCT-23 2OSH 1 REMARK REVDAT 4 18-OCT-17 2OSH 1 REMARK REVDAT 3 24-FEB-09 2OSH 1 VERSN REVDAT 2 04-NOV-08 2OSH 1 JRNL REVDAT 1 03-MAR-07 2OSH 0 JRNL AUTH P.HU,L.SUN,Z.Q.ZHU,X.W.HOU,S.WANG,S.S.YU,H.L.WANG,P.ZHANG, JRNL AUTH 2 M.WANG,L.W.NIU,M.K.TENG,D.Y.RUAN JRNL TITL CRYSTAL STRUCTURE OF NATRATOXIN, A NOVEL SNAKE SECRETED JRNL TITL 2 PHOSPHOLIPASEA2 NEUROTOXIN FROM NAJA ATRA VENOM INHIBITING JRNL TITL 3 A-TYPE K+ CURRENTS. JRNL REF PROTEINS V. 72 673 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18247353 JRNL DOI 10.1002/PROT.21964 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 5557 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 266 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 389 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 21 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 908 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -1.01000 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): 0.357 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.234 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.232 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 936 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1273 ; 1.244 ; 1.928 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 118 ; 5.652 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;32.077 ;24.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 138 ;16.416 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;18.517 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 128 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 738 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 439 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 639 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 55 ; 0.178 ; 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): 51 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.333 ; 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): 607 ; 0.706 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 933 ; 1.205 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 395 ; 1.686 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 340 ; 2.436 ; 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 2OSH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041530. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5557 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 2.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.12700 REMARK 200 R SYM FOR SHELL (I) : 0.12700 REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1MF4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 5% V/V ISO REMARK 280 -PROPANO, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 32.05850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.02925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.08775 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 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 38 -170.66 -172.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 2OSH A 1 119 UNP P00598 PA21_NAJAT 28 146 SEQRES 1 A 119 ASN LEU TYR GLN PHE LYS ASN MET ILE GLN CYS THR VAL SEQRES 2 A 119 PRO SER ARG SER TRP CYS ASP PHE ALA ASP TYR GLY CYS SEQRES 3 A 119 TYR CYS GLY LYS 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 GLY CYS TRP PRO TYR PHE LYS SEQRES 6 A 119 THR TYR SER TYR GLU CYS SER GLN GLY THR LEU THR CYS SEQRES 7 A 119 LYS GLY GLY ASN ASN ALA CYS ALA ALA ALA 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 THR ASP ALA ASN TYR ASN ILE ASP LEU LYS ALA ARG SEQRES 10 A 119 CYS GLN FORMUL 2 HOH *65(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 ASN A 83 ALA A 103 1 21 HELIX 5 5 THR A 106 TYR A 110 5 5 HELIX 6 6 ASP A 113 CYS A 118 1 6 SHEET 1 A 2 TYR A 69 SER A 72 0 SHEET 2 A 2 THR A 75 CYS A 78 -1 O THR A 77 N GLU A 70 SSBOND 1 CYS A 11 CYS A 71 1555 1555 1.99 SSBOND 2 CYS A 26 CYS A 118 1555 1555 2.01 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 2.04 SSBOND 6 CYS A 60 CYS A 85 1555 1555 2.02 SSBOND 7 CYS A 78 CYS A 90 1555 1555 2.05 CRYST1 42.078 42.078 64.117 90.00 90.00 90.00 P 41 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 0.023765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015596 0.00000