HEADER TOXIN 13-JUL-94 1KBA
TITLE CRYSTAL STRUCTURE OF KAPPA-BUNGAROTOXIN AT 2.3-ANGSTROM RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: KAPPA-BUNGAROTOXIN;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BUNGARUS MULTICINCTUS;
SOURCE 3 ORGANISM_COMMON: MANY-BANDED KRAIT;
SOURCE 4 ORGANISM_TAXID: 8616
KEYWDS TOXIN
EXPDTA X-RAY DIFFRACTION
AUTHOR J.C.DEWAN,G.A.GRANT,J.C.SACCHETTINI
REVDAT 5 14-AUG-19 1KBA 1 REMARK
REVDAT 4 17-JUL-19 1KBA 1 REMARK
REVDAT 3 24-FEB-09 1KBA 1 VERSN
REVDAT 2 30-SEP-03 1KBA 1 JRNL DBREF
REVDAT 1 20-DEC-94 1KBA 0
JRNL AUTH J.C.DEWAN,G.A.GRANT,J.C.SACCHETTINI
JRNL TITL CRYSTAL STRUCTURE OF KAPPA-BUNGAROTOXIN AT 2.3-A RESOLUTION.
JRNL REF BIOCHEMISTRY V. 33 13147 1994
JRNL REFN ISSN 0006-2960
JRNL PMID 7947721
JRNL DOI 10.1021/BI00248A026
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : TNT
REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 80.0
REMARK 3 NUMBER OF REFLECTIONS : 5354
REMARK 3
REMARK 3 USING DATA ABOVE SIGMA CUTOFF.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : 0.196
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 USING ALL DATA, NO SIGMA CUTOFF.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1002
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 56
REMARK 3
REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT
REMARK 3 BOND LENGTHS (A) : NULL ; NULL ; NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL
REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL
REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL
REMARK 3
REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 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 RESTRAINT LIBRARIES.
REMARK 3 STEREOCHEMISTRY : NULL
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1KBA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000174399.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6602
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0
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) : 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 <I/SIGMA(I)> 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
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.24
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 -X,-Y,Z
REMARK 290 5555 Y,-X+Y,Z
REMARK 290 6555 X-Y,X,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 -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 0.00000
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 0.00000
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 0.00000
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 0.00000
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: DODECAMERIC
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 0.500000 0.866025 0.000000 0.00000
REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 0.00000
REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 0.00000
REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 0.00000
REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 0.00000
REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 6 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 PRO A 7 C - N - CD ANGL. DEV. = -14.1 DEGREES
REMARK 500 PRO A 15 C - N - CD ANGL. DEV. = -47.5 DEGREES
REMARK 500 LEU A 23 CB - CG - CD2 ANGL. DEV. = -12.0 DEGREES
REMARK 500 PRO A 36 C - N - CD ANGL. DEV. = -13.3 DEGREES
REMARK 500 LEU A 57 CB - CG - CD2 ANGL. DEV. = 10.9 DEGREES
REMARK 500 LEU B 4 CA - CB - CG ANGL. DEV. = -18.9 DEGREES
REMARK 500 SER B 6 N - CA - C ANGL. DEV. = 18.8 DEGREES
REMARK 500 PRO B 15 C - N - CD ANGL. DEV. = -16.8 DEGREES
REMARK 500 PRO B 47 C - N - CD ANGL. DEV. = -13.2 DEGREES
REMARK 500 CYS B 59 CA - CB - SG ANGL. DEV. = -14.5 DEGREES
REMARK 500 ASP B 62 CB - CG - OD1 ANGL. DEV. = 6.0 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 SER A 6 -108.12 -7.35
REMARK 500 PHE A 49 95.00 -66.64
REMARK 500 SER A 55 148.35 160.13
REMARK 500 THR A 61 145.46 -177.78
REMARK 500 SER B 6 -69.62 -20.11
REMARK 500 ASN B 16 119.83 -32.02
REMARK 500 ALA B 25 118.82 -160.65
REMARK 500 ASP B 28 -169.97 -126.79
REMARK 500 CYS B 31 5.36 -67.82
REMARK 500 ARG B 34 -36.04 -139.51
REMARK 500 ASN B 52 34.24 -70.45
REMARK 500 LEU B 56 111.35 -162.32
REMARK 500 THR B 60 75.58 -116.98
REMARK 500 ASN B 63 45.11 33.64
REMARK 500 ASN B 65 74.89 -56.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1NBT RELATED DB: PDB
REMARK 900 1NBT REPORTS AN NMR STRUCTURE DETERMINATION FOR KAPPA-BUNGAROTOXIN.
REMARK 900 SEE THE FOLLOWING TWO REFERENCES: M.J.SUTCLIFFE, C.M.DOBSON,
REMARK 900 R.E.OSWALD, "SOLUTION STRUCTURE OF NEURONAL BUNGAROTOXIN DETERMINED
REMARK 900 BY TWO-DIMENSIONAL NMR SPECTROSCOPY: CALCULATION OF TERTIARY
REMARK 900 STRUCTURE USING SYSTEMATIC HOMOLOGOUS MODEL BUILDING, DYNAMICAL
REMARK 900 SIMULATED ANNEALING, AND RESTRAINED MOLECULAR DYNAMICS".
REMARK 900 BIOCHEMISTRY (1992) V. 31, 2962-2970. R.E.OSWALD, M.J.SUTCLIFFE,
REMARK 900 M.BAMBERGER, R.H.LORING, E.BRASWELL, C.M.DOBSON, "SOLUTION
REMARK 900 STRUCTURE OF NEURONAL BUNGAROTOXIN DETERMINED BY TWO-DIMENSIONAL
REMARK 900 NMR SPECTROSCOPY: SEQUENCE-SPECIFIC ASSIGNMENTS, SECONDARY
REMARK 900 STRUCTURE, AND DIMER FORMATION". BIOCHEMISTRY (1991) V. 30, 4901-
REMARK 900 4909.
DBREF 1KBA A 1 66 UNP P01398 NXL1_BUNMU 22 87
DBREF 1KBA B 1 66 UNP P01398 NXL1_BUNMU 22 87
SEQRES 1 A 66 ARG THR CYS LEU ILE SER PRO SER SER THR PRO GLN THR
SEQRES 2 A 66 CYS PRO ASN GLY GLN ASP ILE CYS PHE LEU LYS ALA GLN
SEQRES 3 A 66 CYS ASP LYS PHE CYS SER ILE ARG GLY PRO VAL ILE GLU
SEQRES 4 A 66 GLN GLY CYS VAL ALA THR CYS PRO GLN PHE ARG SER ASN
SEQRES 5 A 66 TYR ARG SER LEU LEU CYS CYS THR THR ASP ASN CYS ASN
SEQRES 6 A 66 HIS
SEQRES 1 B 66 ARG THR CYS LEU ILE SER PRO SER SER THR PRO GLN THR
SEQRES 2 B 66 CYS PRO ASN GLY GLN ASP ILE CYS PHE LEU LYS ALA GLN
SEQRES 3 B 66 CYS ASP LYS PHE CYS SER ILE ARG GLY PRO VAL ILE GLU
SEQRES 4 B 66 GLN GLY CYS VAL ALA THR CYS PRO GLN PHE ARG SER ASN
SEQRES 5 B 66 TYR ARG SER LEU LEU CYS CYS THR THR ASP ASN CYS ASN
SEQRES 6 B 66 HIS
FORMUL 3 HOH *56(H2 O)
HELIX 1 1 PHE A 30 GLY A 35 1 6
SHEET 1 SA 5 ARG A 1 ILE A 5 0
SHEET 2 SA 5 THR A 10 CYS A 14 1
SHEET 3 SA 5 ILE A 20 GLN A 26 1
SHEET 4 SA 5 VAL A 37 VAL A 43 1
SHEET 5 SA 5 ARG A 54 THR A 60 1
SHEET 1 SB 5 ARG B 1 ILE B 5 0
SHEET 2 SB 5 THR B 10 CYS B 14 1
SHEET 3 SB 5 ILE B 20 GLN B 26 1
SHEET 4 SB 5 VAL B 37 VAL B 43 1
SHEET 5 SB 5 ARG B 54 THR B 60 1
SSBOND 1 CYS A 3 CYS A 21 1555 1555 2.03
SSBOND 2 CYS A 14 CYS A 42 1555 1555 2.04
SSBOND 3 CYS A 27 CYS A 31 1555 1555 2.02
SSBOND 4 CYS A 46 CYS A 58 1555 1555 2.03
SSBOND 5 CYS A 59 CYS A 64 1555 1555 2.04
SSBOND 6 CYS B 3 CYS B 21 1555 1555 2.02
SSBOND 7 CYS B 14 CYS B 42 1555 1555 2.02
SSBOND 8 CYS B 27 CYS B 31 1555 1555 2.02
SSBOND 9 CYS B 46 CYS B 58 1555 1555 2.03
SSBOND 10 CYS B 59 CYS B 64 1555 1555 2.04
CRYST1 80.200 80.200 39.600 90.00 90.00 120.00 P 6 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 0.012469 0.007199 0.000000 0.00000
SCALE2 0.000000 0.014398 0.000000 0.00000
SCALE3 0.000000 0.000000 0.025253 0.00000
(ATOM LINES ARE NOT SHOWN.)
END