PDB Short entry for 1SNB HEADER NEUROTOXIN 12-MAR-97 1SNB TITLE STRUCTURE OF SCORPION NEUROTOXIN BMK M8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROTOXIN BMK M8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SCORPION NEUROTOXIN BMK M8, TOXIN BMK-VIII SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESOBUTHUS MARTENSII; SOURCE 3 ORGANISM_COMMON: CHINESE SCORPION; SOURCE 4 ORGANISM_TAXID: 34649; SOURCE 5 ORGAN: TAIL KEYWDS NEUROTOXIN, SODIUM CHANNEL INHIBITOR, SCORPION EXPDTA X-RAY DIFFRACTION AUTHOR D.C.WANG,Z.H.ZENG,H.M.LI REVDAT 4 03-APR-24 1SNB 1 SEQADV REVDAT 3 29-NOV-17 1SNB 1 HELIX REVDAT 2 24-FEB-09 1SNB 1 VERSN REVDAT 1 15-MAY-97 1SNB 0 JRNL AUTH H.M.LI,D.C.WANG,Z.H.ZENG,L.JIN,R.Q.HU JRNL TITL CRYSTAL STRUCTURE OF AN ACIDIC NEUROTOXIN FROM SCORPION JRNL TITL 2 BUTHUS MARTENSII KARSCH AT 1.85 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 261 415 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8780783 JRNL DOI 10.1006/JMBI.1996.0473 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.HOUSSET,C.HABERSETZER-ROCHAT,J.P.ASTIER, REMARK 1 AUTH 2 J.C.FONTECILLA-CAMPS REMARK 1 TITL CRYSTAL STRUCTURE OF TOXIN II FROM THE SCORPION ANDROCTONUS REMARK 1 TITL 2 AUSTRALIS HECTOR REFINED AT 1.3 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 238 88 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.JIN,M.WANG,Z.H.ZENG,R.Q.HU,D.C.WANG REMARK 1 TITL CRYSTALLOGRAPHIC STUDIES ON AN ACIDIC TOXIN FROM SCORPION REMARK 1 TITL 2 BUTHUS MARTENSII KARSCH REMARK 1 REF CHIN.SCI.BULL. V. 38 561 1993 REMARK 1 REFN ISSN 1001-6538 REMARK 1 REFERENCE 3 REMARK 1 AUTH B.ZHAO,M.CARSON,S.E.EALICK,C.E.BUGG REMARK 1 TITL STRUCTURE OF SCORPION TOXIN VARIANT-3 AT 1.2 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 227 239 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.Q.HU,M.WANG,J.N.LIU,K.J.LEI REMARK 1 TITL PURIFICATION AND PARTIAL CHARACTERIZATION OF SEVERAL NEW REMARK 1 TITL 2 NEUROTOXINS FROM EAST-ASIA SCORPION [CHINESE] REMARK 1 REF DONGWUXUE YANJIU V. 10 185 1989 REMARK 1 REFN ISSN 0254-5853 REMARK 1 REFERENCE 5 REMARK 1 AUTH R.J.ALMASSY,J.C.FONTECILLA-CAMPS,F.L.SUDDATH,C.E.BUGG REMARK 1 TITL STRUCTURE OF VARIANT-3 SCORPION NEUROTOXIN FROM CENTRUROIDES REMARK 1 TITL 2 SCULPTURATUS EWING, REFINED AT 1.8 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 170 497 1983 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 6 REMARK 1 AUTH J.C.FONTECILLA-CAMPS,R.J.ALMASSY,F.L.SUDDATH,D.D.WATT, REMARK 1 AUTH 2 C.E.BUGG REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF A PROTEIN FROM SCORPION REMARK 1 TITL 2 VENOM. A NEW STRUCTURAL CLASS OF NEUROTOXINS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 77 6496 1980 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 3615 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 246 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL 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 : 482 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 2.175 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.04 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.200 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SNB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-91 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3802 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.05230 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 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) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 17.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.15 REMARK 200 R MERGE FOR SHELL (I) : 0.11800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.590 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: AAH II REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 19.28000 REMARK 290 SMTRY3 2 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 126 O HOH A 155 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 6 CB - CA - C ANGL. DEV. = -13.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 -168.33 -162.24 REMARK 500 CYS A 63 -130.47 -125.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 1SNB A 1 64 UNP P54135 SCX8_MESMA 1 64 SEQADV 1SNB GLY A 60 UNP P54135 PRO 60 CONFLICT SEQADV 1SNB ARG A 62 UNP P54135 LYS 62 CONFLICT SEQRES 1 A 64 GLY ARG ASP ALA TYR ILE ALA ASP SER GLU ASN CYS THR SEQRES 2 A 64 TYR PHE CYS GLY SER ASN PRO TYR CYS ASN ASP VAL CYS SEQRES 3 A 64 THR GLU ASN GLY ALA LYS SER GLY TYR CYS GLN TRP ALA SEQRES 4 A 64 GLY ARG TYR GLY ASN ALA CYS TYR CYS ILE ASP LEU PRO SEQRES 5 A 64 ALA SER GLU ARG ILE LYS GLU GLY GLY ARG CYS GLY FORMUL 2 HOH *141(H2 O) HELIX 1 H1 ASN A 19 GLU A 28 1 10 SHEET 1 S1 3 ARG A 2 TYR A 5 0 SHEET 2 S1 3 GLY A 43 LEU A 51 -1 O CYS A 48 N ALA A 4 SHEET 3 S1 3 SER A 33 GLY A 40 -1 O SER A 33 N ILE A 49 SSBOND 1 CYS A 12 CYS A 63 1555 1555 2.04 SSBOND 2 CYS A 16 CYS A 36 1555 1555 2.04 SSBOND 3 CYS A 22 CYS A 46 1555 1555 2.03 SSBOND 4 CYS A 26 CYS A 48 1555 1555 2.05 CRYST1 23.320 38.560 29.150 90.00 107.48 90.00 P 1 21 1 2 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 0.042882 0.000000 0.013504 0.00000 SCALE2 0.000000 0.025934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035966 0.00000