HEADER NEUROTOXIN (POST-SYNAPTIC) 08-AUG-80 1NXB TITLE STRUCTURE AND FUNCTION OF SNAKE VENOM CURARIMIMETIC NEUROTOXINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROTOXIN B; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LATICAUDA SEMIFASCIATA; SOURCE 3 ORGANISM_COMMON: BROAD-BANDED BLUE SEA KRAIT; SOURCE 4 ORGANISM_TAXID: 8631 KEYWDS NEUROTOXIN (POST-SYNAPTIC) EXPDTA X-RAY DIFFRACTION AUTHOR D.TSERNOGLOU,G.A.PETSKO REVDAT 6 29-NOV-17 1NXB 1 HELIX REVDAT 5 24-FEB-09 1NXB 1 VERSN REVDAT 4 22-OCT-84 1NXB 1 SEQRES REVDAT 3 30-SEP-83 1NXB 1 REVDAT REVDAT 2 13-JUN-83 1NXB 1 REMARK REVDAT 1 27-JAN-81 1NXB 0 JRNL AUTH D.TSERNOGLOU,G.A.PETSKO,R.A.HUDSON JRNL TITL STRUCTURE AND FUNCTION OF SNAKE VENOM CURARIMIMETIC JRNL TITL 2 NEUROTOXINS. JRNL REF MOL.PHARMACOL. V. 14 710 1978 JRNL REFN ISSN 0026-895X JRNL PMID 683181 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.TSERNOGLOU,G.A.PETSKO,J.E.MCQUEENJUNIOR,J.HERMANS REMARK 1 TITL MOLECULAR GRAPHICS. APPLICATION TO THE STRUCTURE REMARK 1 TITL 2 DETERMINATION OF A SNAKE VENOM NEUROTOXIN REMARK 1 REF SCIENCE V. 197 1378 1977 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.TSERNOGLOU,G.A.PETSKO,A.T.TU REMARK 1 TITL PROTEIN SEQUENCING BY COMPUTER GRAPHICS REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V. 491 605 1977 REMARK 1 REFN ISSN 0006-3002 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.TSERNOGLOU,G.A.PETSKO REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF NEUROTOXIN A FROM VENOM OF REMARK 1 TITL 2 THE PHILIPPINES SEA SNAKE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 74 971 1977 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 4 REMARK 1 AUTH D.TSERNOGLOU,G.A.PETSKO REMARK 1 TITL THE CRYSTAL STRUCTURE OF A POST-SYNAPTIC NEUROTOXIN FROM SEA REMARK 1 TITL 2 SNAKE AT 2.2 ANGSTROMS RESOLUTION REMARK 1 REF FEBS LETT. V. 68 1 1976 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 472 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 67 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NXB 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_1000175407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 10.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.30000 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 400 REMARK 400 COMPOUND REMARK 400 THE PROTEIN IS PROBABLY IDENTICAL TO ERABUTOXIN FROM REMARK 400 JAPANESE SEA SNAKES. THIS POINT IS DISCUSSED IN REFERENCES REMARK 400 3 AND 4 ABOVE. 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 VAL A 59 CB CG1 CG2 REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 COORDINATES FOR TWO SULFATE IONS ARE INCLUDED BELOW. THERE REMARK 600 IS PROBABLY AT LEAST ONE OTHER BOUND SULFATE WHICH IS REMARK 600 INCLUDED BELOW AS A WATER MOLECULE. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SO4 A 64 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AMS REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES FORMING THE PUTATIVE REMARK 800 ACETYLCHOLINEMIMETIC SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: ETS REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ESSENTIAL TRYPTOPHAN REMARK 800 REMARK 800 SITE_IDENTIFIER: ELS REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES FORMING THE ESSENTIAL LYSINE SURFACE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 63 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 64 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE NUMBERING IS SEQUENTIAL. IN PUBLISHED PAPERS A REMARK 999 GENERAL HOMOLOGY SEQUENCE NUMBERING IS USED OFTEN INSTEAD REMARK 999 OF SEQUENTIAL NUMBERING OF RESIDUES. SEE REFERENCE 1 FOR REMARK 999 DETAILS. REMARK 999 REMARK 999 RESIDUE 59 IS PROBABLY VALINE BUT THIS IS STILL UNDER REMARK 999 INVESTIGATION. RESIDUES 18 AND 19 WERE ORDERED FROM THE REMARK 999 2.2 AND 1.38 ANGSTROM MAPS AFTER REFINEMENT. THE CHEMICAL REMARK 999 SEQUENCE HAS THEM REVERSED. THE SAME IS TRUE OF RESIDUES REMARK 999 21 AND 22. SEE REFERENCE 3 ABOVE. DBREF 1NXB A 1 62 UNP Q90VW1 NXSB_LATSE 22 83 SEQADV 1NXB GLN A 6 UNP Q90VW1 HIS 27 CONFLICT SEQADV 1NXB HIS A 7 UNP Q90VW1 GLN 28 CONFLICT SEQADV 1NXB HIS A 26 UNP Q90VW1 ASN 47 CONFLICT SEQRES 1 A 62 ARG ILE CYS PHE ASN GLN HIS SER SER GLN PRO GLN THR SEQRES 2 A 62 THR LYS THR CYS SER PRO GLY GLU SER SER CYS TYR HIS SEQRES 3 A 62 LYS GLN TRP SER ASP PHE ARG GLY THR ILE ILE GLU ARG SEQRES 4 A 62 GLY CYS GLY CYS PRO THR VAL LYS PRO GLY ILE LYS LEU SEQRES 5 A 62 SER CYS CYS GLU SER GLU VAL CYS ASN ASN HET SO4 A 63 3 HET SO4 A 64 1 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *67(H2 O) SHEET 1 A 5 THR A 13 CYS A 17 0 SHEET 2 A 5 ILE A 2 HIS A 7 -1 N CYS A 3 O LYS A 15 SHEET 3 A 5 GLY A 34 GLY A 40 -1 O ILE A 37 N SER A 8 SHEET 4 A 5 TYR A 25 ASP A 31 -1 N TYR A 25 O GLY A 40 SHEET 5 A 5 LYS A 51 CYS A 54 -1 N SER A 53 O HIS A 26 SSBOND 1 CYS A 3 CYS A 24 1555 1555 1.95 SSBOND 2 CYS A 17 CYS A 41 1555 1555 1.60 SSBOND 3 CYS A 43 CYS A 54 1555 1555 1.97 SSBOND 4 CYS A 55 CYS A 60 1555 1555 2.14 LINK CG GLU A 58 S SO4 A 63 1555 1555 1.87 LINK CD GLU A 58 S SO4 A 63 1555 1555 1.61 LINK OE2 GLU A 58 S SO4 A 63 1555 1555 1.40 LINK CD GLU A 58 O2 SO4 A 63 1555 1555 2.05 LINK OE2 GLU A 58 O2 SO4 A 63 1555 1555 1.39 SITE 1 AMS 3 ASP A 31 PHE A 32 ARG A 33 SITE 1 ETS 1 TRP A 29 SITE 1 ELS 2 LYS A 27 LYS A 47 SITE 1 AC1 5 ARG A 1 ILE A 2 GLU A 58 HOH A 65 SITE 2 AC1 5 HOH A 129 SITE 1 AC2 3 ASN A 5 LYS A 15 HOH A 82 CRYST1 49.900 46.600 21.300 90.00 90.00 90.00 P 21 21 21 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 0.020040 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.046948 0.00000