PDB Short entry for 1SN4 HEADER TOXIN 11-NOV-98 1SN4 TITLE STRUCTURE OF SCORPION NEUROTOXIN BMK M4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (NEUROTOXIN BMK M4); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BMK-IV 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, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR X.L.HE,H.M.LI,X.Q.LIU,Z.H.ZENG,D.C.WANG REVDAT 6 03-APR-24 1SN4 1 REMARK REVDAT 5 27-DEC-23 1SN4 1 REMARK SEQADV REVDAT 4 04-OCT-17 1SN4 1 REMARK REVDAT 3 24-FEB-09 1SN4 1 VERSN REVDAT 2 29-MAR-05 1SN4 1 DBREF JRNL REMARK MASTER REVDAT 1 17-NOV-99 1SN4 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 TOXINS: JRNL TITL 2 NON-PROLINE CIS PEPTIDE BONDS AND IMPLICATIONS FOR NEW JRNL TITL 3 BINDING SITE SELECTIVITY ON 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 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 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 CRYSTALLOGRAPHIC REMARK 1 TITL 3 STUDIES ON AN ACIDIC TOXIN FROM SCORPION BUTHUS MARTENSII REMARK 1 TITL 4 KARSCH REMARK 1 REF ZOOL.RES.SINICA. V. 10 185 1989 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 M.J.LUO,Y.M.XIONG,M.WANG,D.C.WANG,C.W.CHI REMARK 1 TITL PURIFICATION AND SEQUENCE DETERMINATION OF A NEW NEUTRAL REMARK 1 TITL 2 MAMMALIAN NEUROTOXIN FROM THE SCORPION BUTHUS MARTENSII REMARK 1 TITL 3 KARSCH REMARK 1 REF TOXICON V. 35 723 1997 REMARK 1 REFN ISSN 0041-0101 REMARK 1 REFERENCE 5 REMARK 1 AUTH H.M.LI,D.C.WANG,L.JIN,Z.H.ZENG,R.Q.HU REMARK 1 TITL CRYSTAL STRUCTURE OF AN ACIDIC NEUROTOXIN FROM SCORPION REMARK 1 TITL 2 BUTHUS MARTENSII KARSCH AT 1.85A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 261 415 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 73.5 REMARK 3 NUMBER OF REFLECTIONS : 10577 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 : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 998 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 662 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 72 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 : 488 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 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) : NULL 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) : 1.732 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.38 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.065 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) : 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 : PROTEIN_REP.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-98. REMARK 100 THE DEPOSITION ID IS D_1000000061. 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) : 283.0 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS REMARK 200 DATA SCALING SOFTWARE : WEIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10577 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 21.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.5 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: BMK M1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.25333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.50667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.88000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.13333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 5.62667 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 112 O HOH A 113 1.69 REMARK 500 CB ASN A 19 O HOH A 178 1.95 REMARK 500 CD GLU A 20 O HOH A 186 1.96 REMARK 500 OE2 GLU A 20 O HOH A 186 2.04 REMARK 500 CD1 ILE A 6 O HOH A 177 2.12 REMARK 500 O HOH A 151 O HOH A 182 2.13 REMARK 500 CA PRO A 52 O HOH A 169 2.16 REMARK 500 O HOH A 105 O HOH A 128 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 173 O HOH A 184 4665 1.95 REMARK 500 O HOH A 88 O HOH A 90 5554 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 65 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 66 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 67 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 68 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 69 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SN1 RELATED DB: PDB DBREF 1SN4 A 1 64 UNP P45698 SCX9_MESMA 15 78 SEQADV 1SN4 GLY A 18 UNP P45698 THR 32 CONFLICT SEQADV 1SN4 ASP A 54 UNP P45698 ARG 68 CONFLICT SEQRES 1 A 64 VAL ARG ASP ALA TYR ILE ALA LYS PRO GLU ASN CYS VAL SEQRES 2 A 64 TYR HIS CYS ALA GLY ASN GLU GLY CYS ASN LYS LEU CYS SEQRES 3 A 64 THR ASP ASN GLY ALA GLU SER GLY TYR CYS GLN TRP GLY SEQRES 4 A 64 GLY ARG TYR GLY ASN ALA CYS TRP CYS ILE LYS LEU PRO SEQRES 5 A 64 ASP ASP VAL PRO ILE ARG VAL PRO GLY LYS CYS HIS HET ACT A 65 4 HET ACT A 66 4 HET ACT A 67 4 HET ACT A 68 4 HET ACT A 69 4 HETNAM ACT ACETATE ION FORMUL 2 ACT 5(C2 H3 O2 1-) FORMUL 7 HOH *117(H2 O) HELIX 1 1 GLY A 18 ASN A 29 1 12 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 39 -1 O SER A 33 N ILE A 49 SSBOND 1 CYS A 12 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 16 CYS A 36 1555 1555 2.01 SSBOND 3 CYS A 22 CYS A 46 1555 1555 2.01 SSBOND 4 CYS A 26 CYS A 48 1555 1555 2.03 CISPEP 1 PRO A 9 GLU A 10 0 -0.50 SITE 1 AC1 10 ASN A 11 CYS A 12 VAL A 13 GLY A 18 SITE 2 AC1 10 ASN A 19 TRP A 38 ARG A 58 CYS A 63 SITE 3 AC1 10 HOH A 70 HOH A 180 SITE 1 AC2 2 ARG A 41 HOH A 120 SITE 1 AC3 4 HOH A 172 HOH A 174 HOH A 181 HOH A 185 SITE 1 AC4 1 HOH A 95 SITE 1 AC5 3 LYS A 50 HIS A 64 HOH A 146 CRYST1 54.880 54.880 33.760 90.00 90.00 120.00 P 61 6 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 0.018221 0.010520 0.000000 0.00000 SCALE2 0.000000 0.021040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029621 0.00000