HEADER TOXIN 28-FEB-03 1ONJ TITLE CRYSTAL STRUCTURE OF ATRATOXIN-B FROM CHINESE COBRA VENOM OF NAJA ATRA COMPND MOL_ID: 1; COMPND 2 MOLECULE: COBROTOXIN B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATRATOXIN-B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA ATRA; SOURCE 3 ORGANISM_COMMON: CHINESE COBRA; SOURCE 4 ORGANISM_TAXID: 8656 KEYWDS BETA-TURN-BETA, THREE-FINGER PROTEIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR X.LOU,X.TU,G.PAN,C.XU,R.FAN,W.LU,W.DENG,P.RAO,M.TENG,L.NIU REVDAT 4 06-NOV-24 1ONJ 1 REMARK REVDAT 3 11-OCT-17 1ONJ 1 REMARK REVDAT 2 24-FEB-09 1ONJ 1 VERSN REVDAT 1 28-FEB-04 1ONJ 0 JRNL AUTH X.LOU,X.TU,G.PAN,C.XU,R.FAN,W.LU,W.DENG,P.RAO,M.TENG,L.NIU JRNL TITL PURIFICATION, N-TERMINAL SEQUENCING, CRYSTALLIZATION AND JRNL TITL 2 PRELIMINARY STRUCTURAL DETERMINATION OF ATRATOXIN-B, A JRNL TITL 3 SHORT-CHAIN ALPHA-NEUROTOXIN FROM NAJA ATRA VENOM. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 1038 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 12777767 JRNL DOI 10.1107/S0907444903005687 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 7984 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 841 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 472 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ONJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018473. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRL REMARK 200 BEAMLINE : U7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1516 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : MARFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8222 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.555 REMARK 200 RESOLUTION RANGE LOW (A) : 16.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 23.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS-HCL, PH 8.5, REMARK 280 EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.29000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.55500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.55500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.14500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.55500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.55500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.43500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.55500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.55500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.14500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.55500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.55500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.43500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 22.29000 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 SER A 8 -117.61 35.78 REMARK 500 SER A 8 -117.61 35.78 REMARK 500 SER A 18 63.83 -116.28 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 1001 DBREF 1ONJ A 1 61 UNP P80958 NSXB_NAJAT 22 82 SEQRES 1 A 61 LEU GLU CYS HIS ASN GLN GLN SER SER GLN THR PRO THR SEQRES 2 A 61 THR LYS THR CYS SER GLY GLU THR ASN CYS TYR LYS LYS SEQRES 3 A 61 TRP TRP SER ASP HIS ARG GLY THR ILE ILE GLU ARG GLY SEQRES 4 A 61 CYS GLY CYS PRO LYS VAL LYS PRO GLY VAL ASN LEU ASN SEQRES 5 A 61 CYS CYS THR THR ASP ARG CYS ASN ASN HET SO4 A1001 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *84(H2 O) SHEET 1 A 2 GLU A 2 HIS A 4 0 SHEET 2 A 2 THR A 14 THR A 16 -1 O LYS A 15 N CYS A 3 SHEET 1 B 3 GLY A 33 CYS A 40 0 SHEET 2 B 3 CYS A 23 ASP A 30 -1 N TRP A 28 O ILE A 35 SHEET 3 B 3 ASN A 50 CYS A 54 -1 O ASN A 50 N TRP A 27 SSBOND 1 CYS A 3 CYS A 23 1555 1555 2.03 SSBOND 2 CYS A 17 CYS A 40 1555 1555 2.03 SSBOND 3 CYS A 42 CYS A 53 1555 1555 2.03 SSBOND 4 CYS A 54 CYS A 59 1555 1555 2.02 SITE 1 AC1 6 GLN A 7 ASP A 30 HIS A 31 LYS A 44 SITE 2 AC1 6 HOH A 127 HOH A 164 CRYST1 49.110 49.110 44.580 90.00 90.00 90.00 P 41 21 2 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 0.020362 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022432 0.00000