10 20 30 40 50 60 70 80 1R1G - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN 23-SEP-03 1R1G
TITLE CRYSTAL STRUCTURE OF THE SCORPION TOXIN BMBKTTX1
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROTOXIN BMK37; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BMBKTTX1; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE CORRESPONDS TO THAT OF NATURALLY SOURCE 4 OCCURING TOXIN FROM SCORPION BUTHUS MARTENSI KARSCH. SOURCE 5 PROTEIN WAS SYNTHESIZED USING BOC CHEMISTRY. AFTER FOLDING SOURCE 6 ALL PRIMARY AMINO GROUPS OF BMBKTTX1 (FIVE LYSINE RESIDUES SOURCE 7 AND THE N-TERMINUS) WERE DIMETHYLATED.
KEYWDS SIRAS FROM S ATOMS, SCORPION TOXIN, BMBKTTX1, REDUCTIVE KEYWDS 2 DIMETHYLATION
EXPDTA X-RAY DIFFRACTION
AUTHOR A.SZYK,W.LU,C.XU,J.LUBKOWSKI
REVDAT 2 24-FEB-09 1R1G 1 VERSN REVDAT 1 02-MAR-04 1R1G 0
JRNL AUTH A.SZYK,W.LU,C.XU,J.LUBKOWSKI JRNL TITL STRUCTURE OF THE SCORPION TOXIN BMBKTTX1 SOLVED JRNL TITL 2 FROM SINGLE WAVELENGTH ANOMALOUS SCATTERING OF JRNL TITL 3 SULFUR. JRNL REF J.STRUCT.BIOL. V. 145 289 2004 JRNL REFN ISSN 1047-8477 JRNL PMID 14960379 JRNL DOI 10.1016/J.JSB.2003.11.012
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.65 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) (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 5028 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 272 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 765 REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 45 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.94000 REMARK 3 B22 (A**2) : -1.59000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.04 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.68 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.720 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.160 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.590 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.490 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 77.96 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1R1G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-03. REMARK 100 THE RCSB ID CODE IS RCSB020321.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5478 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : HKL-2000, XPREP REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5028 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 12.600 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : 0.03600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 65.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : 0.08900 REMARK 200 R SYM FOR SHELL (I) : 0.08900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 19.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXD, SHARP, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.0K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.84750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: BIOLOGICALLY ACTIVE FORM OF BMBKTX1 IS A MONOMER.
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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 LAL A 1 CH1 CH2 REMARK 470 LAL B 1 CH1 CH2
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q2K RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF BMBKTTX1
REMARK 999 REMARK 999 SEQUENCE REMARK 999 ALL PRIMARY AMINO GROUPS (FIVE LYSINE RESIDUES REMARK 999 AND THE N-TERMINUS) WERE DIMETHYLATED. REMARK 999 DENSITY WAS NOT SUFFICIENT TO MODEL THE METHYL REMARK 999 GROUPS FOR THE N-TERMINUS.
DBREF 1R1G A 1 31 UNP P83407 SCBX_MESMA 1 31 DBREF 1R1G B 1 31 UNP P83407 SCBX_MESMA 1 31
SEQADV 1R1G LAL A 1 UNP P83407 ALA 1 SEE REMARK 999 SEQADV 1R1G MLY A 11 UNP P83407 LYS 11 SEE REMARK 999 SEQADV 1R1G MLY A 21 UNP P83407 LYS 21 SEE REMARK 999 SEQADV 1R1G MLY A 26 UNP P83407 LYS 26 SEE REMARK 999 SEQADV 1R1G MLY A 28 UNP P83407 LYS 28 SEE REMARK 999 SEQADV 1R1G MLY A 31 UNP P83407 LYS 31 SEE REMARK 999 SEQADV 1R1G LAL B 1 UNP P83407 ALA 1 SEE REMARK 999 SEQADV 1R1G MLY B 11 UNP P83407 LYS 11 SEE REMARK 999 SEQADV 1R1G MLY B 21 UNP P83407 LYS 21 SEE REMARK 999 SEQADV 1R1G MLY B 26 UNP P83407 LYS 26 SEE REMARK 999 SEQADV 1R1G MLY B 28 UNP P83407 LYS 28 SEE REMARK 999 SEQADV 1R1G MLY B 31 UNP P83407 LYS 31 SEE REMARK 999
SEQRES 1 A 31 LAL ALA CYS TYR SER SER ASP CYS ARG VAL MLY CYS VAL SEQRES 2 A 31 ALA MET GLY PHE SER SER GLY MLY CYS ILE ASN SER MLY SEQRES 3 A 31 CYS MLY CYS TYR MLY SEQRES 1 B 31 LAL ALA CYS TYR SER SER ASP CYS ARG VAL MLY CYS VAL SEQRES 2 B 31 ALA MET GLY PHE SER SER GLY MLY CYS ILE ASN SER MLY SEQRES 3 B 31 CYS MLY CYS TYR MLY
MODRES 1R1G LAL A 1 ALA N,N-DIMETHYL-L-ALANINE MODRES 1R1G MLY A 11 LYS N-DIMETHYL-LYSINE MODRES 1R1G MLY A 21 LYS N-DIMETHYL-LYSINE MODRES 1R1G MLY A 26 LYS N-DIMETHYL-LYSINE MODRES 1R1G MLY A 28 LYS N-DIMETHYL-LYSINE MODRES 1R1G MLY A 31 LYS N-DIMETHYL-LYSINE MODRES 1R1G LAL B 1 ALA N,N-DIMETHYL-L-ALANINE MODRES 1R1G MLY B 11 LYS N-DIMETHYL-LYSINE MODRES 1R1G MLY B 21 LYS N-DIMETHYL-LYSINE MODRES 1R1G MLY B 26 LYS N-DIMETHYL-LYSINE MODRES 1R1G MLY B 28 LYS N-DIMETHYL-LYSINE MODRES 1R1G MLY B 31 LYS N-DIMETHYL-LYSINE
HET LAL A 1 5 HET MLY A 11 11 HET MLY A 21 11 HET MLY A 26 11 HET MLY A 28 11 HET MLY A 31 12 HET LAL B 1 5 HET MLY B 11 11 HET MLY B 21 11 HET MLY B 26 11 HET MLY B 28 11 HET MLY B 31 12
HETNAM LAL N,N-DIMETHYL-L-ALANINE HETNAM MLY N-DIMETHYL-LYSINE
FORMUL 1 LAL 2(C5 H11 N O2) FORMUL 1 MLY 10(C8 H18 N2 O2) FORMUL 3 HOH *108(H2 O)
HELIX 1 1 TYR A 4 MET A 15 1 12 HELIX 2 2 TYR B 4 MET B 15 1 12
SHEET 1 A 2 SER A 19 ILE A 23 0 SHEET 2 A 2 MLY A 26 TYR A 30 -1 O MLY A 28 N MLY A 21 SHEET 1 B 2 SER B 19 ILE B 23 0 SHEET 2 B 2 MLY B 26 TYR B 30 -1 O MLY B 26 N ILE B 23
SSBOND 1 CYS A 3 CYS A 22 1555 1555 2.03 SSBOND 2 CYS A 8 CYS A 27 1555 1555 2.03 SSBOND 3 CYS A 12 CYS A 29 1555 1555 2.04 SSBOND 4 CYS B 3 CYS B 22 1555 1555 2.03 SSBOND 5 CYS B 8 CYS B 27 1555 1555 2.02 SSBOND 6 CYS B 12 CYS B 29 1555 1555 2.03
LINK C LAL A 1 N ALA A 2 1555 1555 1.33 LINK C VAL A 10 N MLY A 11 1555 1555 1.33 LINK C MLY A 11 N CYS A 12 1555 1555 1.33 LINK C GLY A 20 N MLY A 21 1555 1555 1.33 LINK C MLY A 21 N CYS A 22 1555 1555 1.33 LINK C SER A 25 N MLY A 26 1555 1555 1.33 LINK C MLY A 26 N CYS A 27 1555 1555 1.33 LINK C CYS A 27 N MLY A 28 1555 1555 1.33 LINK C MLY A 28 N CYS A 29 1555 1555 1.33 LINK C TYR A 30 N MLY A 31 1555 1555 1.33 LINK C LAL B 1 N ALA B 2 1555 1555 1.33 LINK C VAL B 10 N MLY B 11 1555 1555 1.33 LINK C MLY B 11 N CYS B 12 1555 1555 1.33 LINK C GLY B 20 N MLY B 21 1555 1555 1.33 LINK C MLY B 21 N CYS B 22 1555 1555 1.33 LINK C SER B 25 N MLY B 26 1555 1555 1.33 LINK C MLY B 26 N CYS B 27 1555 1555 1.32 LINK C CYS B 27 N MLY B 28 1555 1555 1.33 LINK C MLY B 28 N CYS B 29 1555 1555 1.33 LINK C TYR B 30 N MLY B 31 1555 1555 1.33
CRYST1 21.397 39.695 29.368 90.00 94.13 90.00 P 1 21 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 0.046736 0.000000 0.003376 0.00000
SCALE2 0.000000 0.025192 0.000000 0.00000
SCALE3 0.000000 0.000000 0.034139 0.00000