HEADER 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 OCCURING SOURCE 4 TOXIN FROM SCORPION BUTHUS MARTENSI KARSCH. PROTEIN WAS SYNTHESIZED SOURCE 5 USING BOC CHEMISTRY. AFTER FOLDING ALL PRIMARY AMINO GROUPS OF SOURCE 6 BMBKTTX1 (FIVE LYSINE RESIDUES AND THE N-TERMINUS) WERE SOURCE 7 DIMETHYLATED. KEYWDS SIRAS FROM S ATOMS, SCORPION TOXIN, BMBKTTX1, REDUCTIVE KEYWDS 2 DIMETHYLATION, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SZYK,W.LU,C.XU,J.LUBKOWSKI REVDAT 3 11-OCT-17 1R1G 1 REMARK 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 FROM SINGLE JRNL TITL 2 WAVELENGTH ANOMALOUS SCATTERING OF 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 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 : 474 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) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.680 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020321. 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 : XPREP REMARK 200 DATA SCALING SOFTWARE : HKL-2000 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 : 12.60 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 : 19.00 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 (%): 30.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 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 HETATM 1 CB LAL A 1 -1.377 7.822 15.018 1.00 24.10 C HETATM 2 C LAL A 1 -0.547 7.775 12.667 1.00 23.64 C HETATM 3 O LAL A 1 -0.340 6.791 11.950 1.00 24.31 O HETATM 4 N LAL A 1 -2.732 6.733 13.267 1.00 24.18 N HETATM 5 CA LAL A 1 -1.786 7.854 13.556 1.00 23.87 C