PDB Short entry for 1B7D HEADER TOXIN 21-JAN-99 1B7D TITLE NEUROTOXIN (TS1) FROM BRAZILIAN SCORPION TITYUS SERRULATUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (NEUROTOXIN TS1); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TITYUS SERRULATUS; SOURCE 3 ORGANISM_COMMON: BRAZILIAN SCORPION; SOURCE 4 ORGANISM_TAXID: 6887; SOURCE 5 SECRETION: VENOM KEYWDS LONG-CHAIN NEUROTOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR I.POLIKARPOV,M.S.SANCHES JR.,S.MARANGONI,M.H.TOYAMA,A.TEPLYAKOV REVDAT 4 09-AUG-23 1B7D 1 REMARK SSBOND REVDAT 3 24-FEB-09 1B7D 1 VERSN REVDAT 2 01-APR-03 1B7D 1 JRNL REVDAT 1 22-JUL-99 1B7D 0 JRNL AUTH I.POLIKARPOV,M.S.JUNIOR,S.MARANGONI,M.H.TOYAMA,A.TEPLYAKOV JRNL TITL CRYSTAL STRUCTURE OF NEUROTOXIN TS1 FROM TITYUS SERRULATUS JRNL TITL 2 PROVIDES INSIGHTS INTO THE SPECIFICITY AND TOXICITY OF JRNL TITL 3 SCORPION TOXINS. JRNL REF J.MOL.BIOL. V. 290 175 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10388565 JRNL DOI 10.1006/JMBI.1999.2868 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.M.GOLUBEV,W.H.LEE,S.MARANGONI,J.C.NOVELLO,B.OLIVEIRA, REMARK 1 AUTH 2 M.H.TOYAMA REMARK 1 TITL CRYSTALLISATION AND PRELIMINARY DIFFRACTION DATA OF REMARK 1 TITL 2 NEUROTOXIN TS-GAMMA FROM THE VENOM OF SCORPION TITYUS REMARK 1 TITL 3 SERRULATUS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 54 1437 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 5149 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 479 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.032 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.032 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.027 ; 0.040 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.144 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.177 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.270 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.181 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 15.000; NULL REMARK 3 PLANAR (DEGREES) : 4.300 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 12.900; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 10.000; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.404 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.380 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.698 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.481 ; 8.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-99. REMARK 100 THE DEPOSITION ID IS D_1000000343. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.37 REMARK 200 MONOCHROMATOR : SI BENT SINGLE-CRYSTAL REMARK 200 OPTICS : CYLINDRICAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 13.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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: PDB ENTRY 1AHO REMARK 200 REMARK 200 REMARK: REMARK 200 DIFFRACTION DATA HAVE BEEN COLLECTED AT THE LABORATORIO NACIONAL REMARK 200 DE LUZ REMARK 200 SINCROTRON (LNLS), CAMPINAS, BRAZIL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0 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 18.27000 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: 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 CYS A 27 CA - CB - SG ANGL. DEV. = 9.4 DEGREES REMARK 500 TYR A 36 CB - CG - CD2 ANGL. DEV. = 3.7 DEGREES REMARK 500 TYR A 43 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 CYS A 44 CA - CB - SG ANGL. DEV. = 8.7 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 LYS A 31 16.11 84.00 REMARK 500 TRP A 39 128.00 -35.39 REMARK 500 LYS A 60 -128.68 -108.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 60 -11.58 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 PO4 A 66 DBREF 1B7D A 1 61 UNP P15226 SCX7_TITSE 21 81 SEQRES 1 A 61 LYS GLU GLY TYR LEU MET ASP HIS GLU GLY CYS LYS LEU SEQRES 2 A 61 SER CYS PHE ILE ARG PRO SER GLY TYR CYS GLY ARG GLU SEQRES 3 A 61 CYS GLY ILE LYS LYS GLY SER SER GLY TYR CYS ALA TRP SEQRES 4 A 61 PRO ALA CYS TYR CYS TYR GLY LEU PRO ASN TRP VAL LYS SEQRES 5 A 61 VAL TRP ASP ARG ALA THR ASN LYS CYS HET PO4 A 66 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *65(H2 O) HELIX 1 1 TYR A 22 LYS A 30 1 9 SHEET 1 A 2 SER A 34 ALA A 38 0 SHEET 2 A 2 ALA A 41 TYR A 45 -1 N TYR A 45 O SER A 34 SSBOND 1 CYS A 11 CYS A 61 1555 1555 2.04 SSBOND 2 CYS A 15 CYS A 37 1555 1555 1.99 SSBOND 3 CYS A 23 CYS A 42 1555 1555 2.02 SSBOND 4 CYS A 27 CYS A 44 1555 1555 2.01 CISPEP 1 TRP A 39 PRO A 40 0 9.16 SITE 1 AC1 6 LYS A 1 ASN A 49 HOH A 74 HOH A 93 SITE 2 AC1 6 HOH A 95 HOH A 117 CRYST1 22.210 36.540 31.720 90.00 100.76 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 0.045025 0.000000 0.008556 0.00000 SCALE2 0.000000 0.027367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032090 0.00000