HEADER TOXIN 09-MAY-04 1T7B TITLE CRYSTAL STRUCTURE OF MUTANT LYS8GLN OF SCORPION ALPHA-LIKE NEUROTOXIN TITLE 2 BMK M1 FROM BUTHUS MARTENSII KARSCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-LIKE NEUROTOXIN BMK-I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BMK M1, BMK I, BMKI, BMK1, BMK-M1, BMKM1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESOBUTHUS MARTENSII; SOURCE 3 ORGANISM_COMMON: CHINESE SCORPION; SOURCE 4 ORGANISM_TAXID: 34649; SOURCE 5 GENE: BMK M1; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: S-78; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PVT 102U-ALPHA KEYWDS BMK M1 MUTANT, SCORPION TOXIN, BUTHUS MARTENSII KARSCH, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIANG,R.J.GUAN,X.L.HE,C.G.WANG,M.WANG,Y.ZHANG,E.J.SUNDBERG,D.C.WANG REVDAT 6 16-OCT-24 1T7B 1 REMARK REVDAT 5 25-OCT-23 1T7B 1 REMARK REVDAT 4 10-NOV-21 1T7B 1 SEQADV REVDAT 3 08-AUG-18 1T7B 1 REMARK REVDAT 2 24-FEB-09 1T7B 1 VERSN REVDAT 1 07-SEP-04 1T7B 0 JRNL AUTH R.J.GUAN,Y.XIANG,X.L.HE,C.G.WANG,M.WANG,Y.ZHANG, JRNL AUTH 2 E.J.SUNDBERG,D.C.WANG JRNL TITL STRUCTURAL MECHANISM GOVERNING CIS AND TRANS ISOMERIC STATES JRNL TITL 2 AND AN INTRAMOLECULAR SWITCH FOR CIS/TRANS ISOMERIZATION OF JRNL TITL 3 A NON-PROLINE PEPTIDE BOND OBSERVED IN CRYSTAL STRUCTURES OF JRNL TITL 4 SCORPION TOXINS JRNL REF J.MOL.BIOL. V. 341 1189 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15321715 JRNL DOI 10.1016/J.JMB.2004.06.067 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.L.HE,H.M.LI,Z.H.ZENG,X.Q.LIU,M.WANG,D.C.WANG REMARK 1 TITL CRYSTAL STRUCTURES OF TWO ALPHA-LIKE SCORPION TOXINS: REMARK 1 TITL 2 NON-PROLINE CIS PEPTIDE BONDS AND IMPLICATIONS FOR NEW REMARK 1 TITL 3 BINDING SITE SELECTIVITY ON THE SODIUM CHANNEL REMARK 1 REF J.MOL.BIOL. V. 292 125 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10493862 REMARK 1 DOI 10.1006/JMBI.1999.3036 REMARK 1 REFERENCE 2 REMARK 1 AUTH F.SHAO,Y.M.XIONG,R.H.ZHU,M.H.LING,C.W.CHI,D.C.WANG REMARK 1 TITL EXPRESSION AND PURIFICATION OF THE BMK M1 NEUROTOXIN FROM REMARK 1 TITL 2 THE SCORPION BUTHUS MARTENSII KARSCH REMARK 1 REF PROTEIN EXPR.PURIF. V. 17 358 1999 REMARK 1 REFN ISSN 1046-5928 REMARK 1 PMID 10600453 REMARK 1 DOI 10.1006/PREP.1999.1127 REMARK 1 REFERENCE 3 REMARK 1 AUTH Y.M.XIONG,M.H.LING,D.C.WANG,C.W.CHI REMARK 1 TITL THE CDNA AND GENOMIC DNA SEQUENCES OF A MAMMALIAN NEUROTOXIN REMARK 1 TITL 2 FROM THE SCORPION BUTHUS MARTENSII KARSCH REMARK 1 REF TOXICON V. 35 1025 1997 REMARK 1 REFN ISSN 0041-0101 REMARK 1 PMID 9248001 REMARK 1 DOI 10.1016/S0041-0101(96)00224-3 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 550329.310 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 4831 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) : 0.170 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.500 REMARK 3 FREE R VALUE TEST SET COUNT : 401 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 649 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 517 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.11000 REMARK 3 B22 (A**2) : 1.77000 REMARK 3 B33 (A**2) : 0.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.060 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) : 1.350 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.100 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.060 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.980 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 32.81 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_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T7B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4831 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : 0.28300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1SN1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, SODIUM CACODYLATE, AMMONIUM REMARK 280 SULFATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 23.79450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.02800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.79450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.02800 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 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 33 -179.47 -170.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SN1 RELATED DB: PDB REMARK 900 STRUCTURE OF SCORPION NEUROTOXIN BMK M1 REMARK 900 RELATED ID: 1T7A RELATED DB: PDB REMARK 900 THE SAME PROTEIN, K8D MUTANT REMARK 900 RELATED ID: 1T7E RELATED DB: PDB REMARK 900 THE SAME PROTEIN, P9S MUTANT DBREF 1T7B A 1 64 UNP P45697 SCX1_MESMA 20 83 SEQADV 1T7B ASN A 65 UNP P45697 CLONING ARTIFACT SEQADV 1T7B SER A 66 UNP P45697 CLONING ARTIFACT SEQADV 1T7B GLN A 8 UNP P45697 LYS 27 ENGINEERED MUTATION SEQRES 1 A 66 ASN SER VAL ARG ASP ALA TYR ILE ALA GLN PRO HIS ASN SEQRES 2 A 66 CYS VAL TYR GLU CYS ALA ARG ASN GLU TYR CYS ASN ASP SEQRES 3 A 66 LEU CYS THR LYS ASN GLY ALA LYS SER GLY TYR CYS GLN SEQRES 4 A 66 TRP VAL GLY LYS TYR GLY ASN GLY CYS TRP CYS ILE GLU SEQRES 5 A 66 LEU PRO ASP ASN VAL PRO ILE ARG VAL PRO GLY LYS CYS SEQRES 6 A 66 HIS FORMUL 2 HOH *50(H2 O) HELIX 1 1 ARG A 18 ASN A 29 1 12 SHEET 1 A 3 VAL A 1 TYR A 5 0 SHEET 2 A 3 GLY A 45 PRO A 52 -1 O CYS A 48 N ALA A 4 SHEET 3 A 3 SER A 33 GLN A 37 -1 N TYR A 35 O TRP A 47 SHEET 1 B 2 ALA A 7 GLN A 8 0 SHEET 2 B 2 CYS A 12 VAL A 13 -1 O CYS A 12 N GLN A 8 SSBOND 1 CYS A 12 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 16 CYS A 36 1555 1555 2.03 SSBOND 3 CYS A 22 CYS A 46 1555 1555 2.02 SSBOND 4 CYS A 26 CYS A 48 1555 1555 2.02 CISPEP 1 PRO A 9 HIS A 10 0 0.00 CRYST1 47.589 44.056 25.510 90.00 90.00 90.00 P 21 21 2 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 0.021013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022698 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039200 0.00000