HEADER TOXIN 06-JUL-00 1F94
TITLE THE 0.97 RESOLUTION STRUCTURE OF BUCANDIN, A NOVEL TOXIN ISOLATED FROM
TITLE 2 THE MALAYAN KRAIT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BUCANDIN;
COMPND 3 CHAIN: A
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BUNGARUS CANDIDUS;
SOURCE 3 ORGANISM_TAXID: 92438;
SOURCE 4 SECRETION: VENOM
KEYWDS THREE-FINGER SNAKE PRESYNAPTIC NEUROTOXIN, TOXIN
EXPDTA X-RAY DIFFRACTION
AUTHOR P.KUHN,A.M.DEACON,S.COMOSO,G.RAJASEGER,R.M.KINI,I.USON,P.R.KOLATKAR
REVDAT 5 04-OCT-17 1F94 1 REMARK
REVDAT 4 24-FEB-09 1F94 1 VERSN
REVDAT 3 15-MAR-05 1F94 1 REMARK JRNL ATOM MASTER
REVDAT 2 03-NOV-00 1F94 1 JRNL
REVDAT 1 26-JUL-00 1F94 0
JRNL AUTH P.KUHN,A.M.DEACON,S.COMOSO,G.RAJASEGER,R.M.KINI,I.USON,
JRNL AUTH 2 P.R.KOLATKAR
JRNL TITL THE ATOMIC RESOLUTION STRUCTURE OF BUCANDIN, A NOVEL TOXIN
JRNL TITL 2 ISOLATED FROM THE MALAYAN KRAIT, DETERMINED BY DIRECT
JRNL TITL 3 METHODS.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 1401 2000
JRNL REFN ISSN 0907-4449
JRNL PMID 11053837
JRNL DOI 10.1107/S0907444900011501
REMARK 2
REMARK 2 RESOLUTION. 0.97 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELXL-97
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : 5% RANDOM (WITH SHELXPRO)
REMARK 3 ALL REFLECTIONS INCLUDED ON
REMARK 3 LAST REFINEMENT CYCLE
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.123
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.123
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.177
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1636
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 33339
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 498
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 118
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL
REMARK 3 NUMBER OF RESTRAINTS : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.017
REMARK 3 ANGLE DISTANCES (A) : 2.260
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1F94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-00.
REMARK 100 THE DEPOSITION ID IS D_1000011395.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-MAR-99
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL9-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.98
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33370
REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970
REMARK 200 RESOLUTION RANGE LOW (A) : 32.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 3.500
REMARK 200 R MERGE (I) : 0.05400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7
REMARK 200 DATA REDUNDANCY IN SHELL : 3.00
REMARK 200 R MERGE FOR SHELL (I) : 0.66000
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: NULL
REMARK 200 SOFTWARE USED: SNB, SHELX
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 35.47
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: ISO-PROPANOL, AMMONIUM ACETATE, TRIS,
REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -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 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.48500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.26000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.48500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.26000
REMARK 290 SMTRY3 4 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: 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 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 A 183 LIES ON A SPECIAL POSITION.
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU A 20 CG CD OE1 OE2
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 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 TRP A 27 CA - CB - CG ANGL. DEV. = 11.7 DEGREES
REMARK 500 TRP A 27 CH2 - CZ2 - CE2 ANGL. DEV. = 6.1 DEGREES
REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 GLU A 45 CA - CB - CG ANGL. DEV. = -13.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1F94 A 1 63 UNP P81782 BUCA_BUNCA 1 63
SEQRES 1 A 63 MET GLU CYS TYR ARG CYS GLY VAL SER GLY CYS HIS LEU
SEQRES 2 A 63 LYS ILE THR CYS SER ALA GLU GLU THR PHE CYS TYR LYS
SEQRES 3 A 63 TRP LEU ASN LYS ILE SER ASN GLU ARG TRP LEU GLY CYS
SEQRES 4 A 63 ALA LYS THR CYS THR GLU ILE ASP THR TRP ASN VAL TYR
SEQRES 5 A 63 ASN LYS CYS CYS THR THR ASN LEU CYS ASN THR
FORMUL 2 HOH *118(H2 O)
SHEET 1 A 2 GLU A 2 GLY A 7 0
SHEET 2 A 2 GLY A 10 THR A 16 -1 O GLY A 10 N GLY A 7
SHEET 1 B 4 ARG A 35 ALA A 40 0
SHEET 2 B 4 PHE A 23 ASN A 29 -1 O PHE A 23 N ALA A 40
SHEET 3 B 4 VAL A 51 CYS A 56 -1 O TYR A 52 N LEU A 28
SHEET 4 B 4 ILE A 46 ASP A 47 -1 O ILE A 46 N ASN A 53
SSBOND 1 CYS A 3 CYS A 24 1555 1555 2.02
SSBOND 2 CYS A 6 CYS A 11 1555 1555 2.06
SSBOND 3 CYS A 17 CYS A 39 1555 1555 2.06
SSBOND 4 CYS A 43 CYS A 55 1555 1555 2.03
SSBOND 5 CYS A 56 CYS A 61 1555 1555 2.04
CRYST1 76.970 22.520 32.600 90.00 100.23 90.00 C 1 2 1 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 0.012992 0.000000 0.002345 0.00000
SCALE2 0.000000 0.044405 0.000000 0.00000
SCALE3 0.000000 0.000000 0.031170 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
