10 20 30 40 50 60 70 80 1SN1 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN 12-NOV-98 1SN1
TITLE STRUCTURE OF SCORPION NEUROTOXIN BMK M1
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (NEUROTOXIN BMK M1); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SCORPION NEUROTOXIN BMK M1, TOXIN BMK I
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; SOURCE 6 SECRETION: VENOM
KEYWDS NEUROTOXIN, SODIUM CHANNEL INHIBITOR, SCORPION
EXPDTA X-RAY DIFFRACTION
AUTHOR X.L.HE,H.M.LI,X.Q.LIU,Z.H.ZENG,D.C.WANG
REVDAT 3 24-FEB-09 1SN1 1 VERSN REVDAT 2 01-APR-03 1SN1 1 JRNL REVDAT 1 17-NOV-99 1SN1 0
JRNL AUTH X.L.HE,H.M.LI,Z.H.ZENG,X.Q.LIU,M.WANG,D.C.WANG JRNL TITL CRYSTAL STRUCTURES OF TWO ALPHA-LIKE SCORPION JRNL TITL 2 TOXINS: NON-PROLINE CIS PEPTIDE BONDS AND JRNL TITL 3 IMPLICATIONS FOR NEW BINDING SITE SELECTIVITY ON JRNL TITL 4 THE SODIUM CHANNEL. JRNL REF J.MOL.BIOL. V. 292 125 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10493862 JRNL DOI 10.1006/JMBI.1999.3036
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.M.LI,D.C.WANG,Z.H.ZENG,L.JIN,R.Q.HU REMARK 1 TITL CRYSTAL STRUCTURE OF AN ACIDIC NEUROTOXIN FROM REMARK 1 TITL 2 SCORPION BUTHUS MARTENSII KARSCH AT 1.85 A REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 261 415 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.H.JI,P.MANSUELLE,S.TERAKAWA,C.KOPEYAN REMARK 1 TITL TWO NEUROTOXINS (BMK I AND BMK II) FROM THE VENOM REMARK 1 TITL 2 OF THE SCORPION BUTHUS MARTENSII REMARK 1 TITL 3 KARSCH-PURIFICATION, AMINO ACID SEQUENCE AND REMARK 1 TITL 4 ASSESSMENT OF SPECIFIC ACTIVITY REMARK 1 REF TOXICON V. 34 987 1996 REMARK 1 REFN ISSN 0041-0101 REMARK 1 REFERENCE 3 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 REMARK 1 TITL 2 ANDROCTONUS AUSTRALIS HECTOR REFINED AT 1.3 A REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 238 88 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 4 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 REMARK 1 TITL 2 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 227 239 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 5 REMARK 1 AUTH R.Q.HU,M.WANG,J.N.LIU,K.J.LEI REMARK 1 TITL PURIFICATION AND PARTIAL CHARACTERIZATION OF REMARK 1 TITL 2 SEVERAL NEW NEUROTOXINS FROM EAST- ASIA SCORPION REMARK 1 TITL 3 [CHINESE] REMARK 1 REF DONGWUXUE YANJIU V. 10 185 1989 REMARK 1 REFERENCE 6 REMARK 1 AUTH R.J.ALMASSY,J.C.FONTECILLA-CAMPS,F.L.SUDDATH, REMARK 1 AUTH 2 C.E.BUGG REMARK 1 TITL STRUCTURE OF VARIANT-3 SCORPION NEUROTOXIN FROM REMARK 1 TITL 2 CENTRUROIDES SCULPTURATUS EWING, REFINED AT 1.8 A REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 170 496 1983 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 7 REMARK 1 AUTH J.C.FONTECILLA-CAMPS,R.J.ALMASSY,F.L.SUDDATH, REMARK 1 AUTH 2 D.D.WATT,C.E.BUGG REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF A PROTEIN FROM REMARK 1 TITL 2 SCORPION VENOM. A NEW STRUCTURAL CLASS OF REMARK 1 TITL 3 NEUROTOXINS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 77 6496 1980 REMARK 1 REFN ISSN 0027-8424
REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.3 REMARK 3 NUMBER OF REFLECTIONS : 8360 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) : 0.169 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 840 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) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 474 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 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 : 503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.90 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) : 0.15 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) : 1.91 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.28 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.00 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 1SN1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-98. REMARK 100 THE RCSB ID CODE IS RCSB000077.
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) : 293.0 REMARK 200 PH : 7.5 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 : 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 X200B REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8360 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.3 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: BMK M8 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5
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 41.71000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.71000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.54500 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: 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 81 O HOH A 145 1.95 REMARK 500 O HOH A 112 O HOH A 137 2.14 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 LEU A 51 CA - CB - CG ANGL. DEV. = 14.0 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 -179.05 -175.12 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 122 DISTANCE = 5.26 ANGSTROMS REMARK 525 HOH A 154 DISTANCE = 12.00 ANGSTROMS REMARK 525 HOH A 162 DISTANCE = 8.85 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SN4 RELATED DB: PDB
DBREF 1SN1 A 1 64 UNP P45697 SCX1_MESMA 20 83
SEQRES 1 A 64 VAL ARG ASP ALA TYR ILE ALA LYS PRO HIS ASN CYS VAL SEQRES 2 A 64 TYR GLU CYS ALA ARG ASN GLU TYR CYS ASN ASP LEU CYS SEQRES 3 A 64 THR LYS ASN GLY ALA LYS SER GLY TYR CYS GLN TRP VAL SEQRES 4 A 64 GLY LYS TYR GLY ASN GLY CYS TRP CYS ILE GLU LEU PRO SEQRES 5 A 64 ASP ASN VAL PRO ILE ARG VAL PRO GLY LYS CYS HIS
FORMUL 2 HOH *111(H2 O)
HELIX 1 H1 ASN A 19 LYS A 28 1 10
SHEET 1 S1 3 ARG A 2 TYR A 5 0 SHEET 2 S1 3 SER A 33 VAL A 39 -1 SHEET 3 S1 3 GLY A 43 LEU A 51 -1
SSBOND 1 CYS A 12 CYS A 63 1555 1555 2.01 SSBOND 2 CYS A 16 CYS A 36 1555 1555 2.03 SSBOND 3 CYS A 22 CYS A 46 1555 1555 2.03 SSBOND 4 CYS A 26 CYS A 48 1555 1555 2.02
CISPEP 1 PRO A 9 HIS A 10 0 -0.62
CRYST1 83.420 41.090 23.930 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 0.011987 0.000000 0.000000 0.00000
SCALE2 0.000000 0.024337 0.000000 0.00000
SCALE3 0.000000 0.000000 0.041788 0.00000