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 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 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