HEADER CYTOTOXIN 29-AUG-96 1KXI TITLE STRUCTURE OF CYTOTOXIN HOMOLOG PRECURSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARDIOTOXIN V; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CTX A5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA ATRA; SOURCE 3 ORGANISM_COMMON: CHINESE COBRA; SOURCE 4 ORGANISM_TAXID: 8656; SOURCE 5 ORGAN: VENOM GLAND; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VENOM, CYTOTOXIN, CARDIOTOXIN, MULTIGENE FAMILY, SIGNAL EXPDTA X-RAY DIFFRACTION AUTHOR Y.-J.SUN,W.-G.WU,C.-M.CHIANG,A.-Y.HSIN,C.-D.HSIAO REVDAT 2 24-FEB-09 1KXI 1 VERSN REVDAT 1 21-APR-97 1KXI 0 JRNL AUTH Y.J.SUN,W.G.WU,C.M.CHIANG,A.Y.HSIN,C.D.HSIAO JRNL TITL CRYSTAL STRUCTURE OF CARDIOTOXIN V FROM TAIWAN JRNL TITL 2 COBRA VENOM: PH-DEPENDENT CONFORMATIONAL CHANGE JRNL TITL 3 AND A NOVEL MEMBRANE-BINDING MOTIF IDENTIFIED IN JRNL TITL 4 THE THREE-FINGER LOOPS OF P-TYPE CARDIOTOXIN. JRNL REF BIOCHEMISTRY V. 36 2403 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9054545 JRNL DOI 10.1021/BI962594H REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.Y.CHIEN,C.M.CHIANG,Y.C.HSEU,A.A.VYAS,G.S.RULE, REMARK 1 AUTH 2 W.G.WU REMARK 1 TITL TWO DISTINCT TYPES OF CARDIOTOXIN AS REVEALED BY REMARK 1 TITL 2 THE STRUCTURE AND ACTIVITY RELATIONSHIP OF THEIR REMARK 1 TITL 3 INTERACTION WITH ZWITTERIONIC PHOSPHOLIPID REMARK 1 TITL 4 DISPERSIONS REMARK 1 REF J.BIOL.CHEM. V. 269 14473 1994 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.Y.CHIEN,W.N.HUANG,J.H.JEAN,W.G.WU REMARK 1 TITL FUSION OF SPHINGOMYELIN VESICLES INDUCED BY REMARK 1 TITL 2 PROTEINS FROM TAIWAN COBRA (NAJA NAJA ATRA) VENOM. REMARK 1 TITL 3 INTERACTIONS OF ZWITTERIONIC PHOSPHOLIPIDS WITH REMARK 1 TITL 4 CARDIOTOXIN ANALOGUES REMARK 1 REF J.BIOL.CHEM. V. 266 3252 1991 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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 : 7013 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.70 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) : 0.30 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.60 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 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 1KXI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-95 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7280 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 73.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.65000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.95000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.65000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.65000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 110.85000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.65000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.65000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.95000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.65000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.65000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 110.85000 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 73.90000 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: DIMERIC 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 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 LYS A 24 CG - CD - CE ANGL. DEV. = 25.3 DEGREES REMARK 500 LYS B 46 CD - CE - NZ ANGL. DEV. = 20.4 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 LYS A 29 -71.58 -79.68 REMARK 500 PHE A 34 146.07 -170.11 REMARK 500 THR B 6 -166.26 -125.06 REMARK 500 PRO B 16 163.25 -48.44 REMARK 500 LYS B 28 -77.92 -47.46 REMARK 500 PHE B 30 116.08 -163.08 REMARK 500 SER B 48 -161.62 -117.48 REMARK 500 REMARK 500 REMARK: NULL DBREF 1KXI A 1 62 UNP P62375 CXH_NAJAT 22 83 DBREF 1KXI B 1 62 UNP P62375 CXH_NAJAT 22 83 SEQRES 1 A 62 LEU LYS CYS HIS ASN THR GLN LEU PRO PHE ILE TYR LYS SEQRES 2 A 62 THR CYS PRO GLU GLY LYS ASN LEU CYS PHE LYS ALA THR SEQRES 3 A 62 LEU LYS LYS PHE PRO LEU LYS PHE PRO VAL LYS ARG GLY SEQRES 4 A 62 CYS ALA ASP ASN CYS PRO LYS ASN SER ALA LEU LEU LYS SEQRES 5 A 62 TYR VAL CYS CYS SER THR ASP LYS CYS ASN SEQRES 1 B 62 LEU LYS CYS HIS ASN THR GLN LEU PRO PHE ILE TYR LYS SEQRES 2 B 62 THR CYS PRO GLU GLY LYS ASN LEU CYS PHE LYS ALA THR SEQRES 3 B 62 LEU LYS LYS PHE PRO LEU LYS PHE PRO VAL LYS ARG GLY SEQRES 4 B 62 CYS ALA ASP ASN CYS PRO LYS ASN SER ALA LEU LEU LYS SEQRES 5 B 62 TYR VAL CYS CYS SER THR ASP LYS CYS ASN FORMUL 3 HOH *73(H2 O) SHEET 1 A 2 LYS A 2 HIS A 4 0 SHEET 2 A 2 TYR A 12 THR A 14 -1 N LYS A 13 O CYS A 3 SHEET 1 B 2 LEU A 21 ALA A 25 0 SHEET 2 B 2 LYS A 37 ALA A 41 -1 N ALA A 41 O LEU A 21 SHEET 1 C 2 LYS B 2 HIS B 4 0 SHEET 2 C 2 TYR B 12 THR B 14 -1 N LYS B 13 O CYS B 3 SHEET 1 D 3 LYS B 37 ALA B 41 0 SHEET 2 D 3 LEU B 21 LEU B 27 -1 N ALA B 25 O LYS B 37 SHEET 3 D 3 LEU B 51 CYS B 56 -1 N CYS B 56 O CYS B 22 SSBOND 1 CYS A 3 CYS A 22 1555 1555 2.02 SSBOND 2 CYS A 15 CYS A 40 1555 1555 2.02 SSBOND 3 CYS A 44 CYS A 55 1555 1555 2.02 SSBOND 4 CYS A 56 CYS A 61 1555 1555 2.03 SSBOND 5 CYS B 3 CYS B 22 1555 1555 2.02 SSBOND 6 CYS B 15 CYS B 40 1555 1555 2.02 SSBOND 7 CYS B 44 CYS B 55 1555 1555 2.02 SSBOND 8 CYS B 56 CYS B 61 1555 1555 2.04 CRYST1 43.300 43.300 147.800 90.00 90.00 90.00 P 41 21 2 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 0.023095 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023095 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006766 0.00000