PDB Short entry for 3VTS HEADER TOXIN 06-JUN-12 3VTS TITLE CRYSTAL STRUCTURE OF A THREE FINGER TOXIN FROM SNAKE VENOM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOTOXIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HEMOLYTIC PROTEIN 12B, THREE FINGER TOXIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEMACHATUS HAEMACHATUS; SOURCE 3 ORGANISM_COMMON: RINGHALS; SOURCE 4 ORGANISM_TAXID: 8626 KEYWDS THREE FINGER TOXIN, VENOM TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR C.JOBICHEN,J.SIVARAMAN REVDAT 3 08-NOV-23 3VTS 1 REMARK REVDAT 2 27-NOV-13 3VTS 1 JRNL REVDAT 1 07-NOV-12 3VTS 0 JRNL AUTH V.M.GIRISH,S.KUMAR,L.JOSEPH,C.JOBICHEN,R.M.KINI,J.SIVARAMAN JRNL TITL IDENTIFICATION AND STRUCTURAL CHARACTERIZATION OF A NEW JRNL TITL 2 THREE-FINGER TOXIN HEMACHATOXIN FROM HEMACHATUS HAEMACHATUS JRNL TITL 3 VENOM. JRNL REF PLOS ONE V. 7 48112 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 23144733 JRNL DOI 10.1371/JOURNAL.PONE.0048112 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 5614 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.210 REMARK 3 FREE R VALUE TEST SET COUNT : 573 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.1147 - 3.8493 0.93 1265 148 0.1914 0.2082 REMARK 3 2 3.8493 - 3.0562 0.97 1263 138 0.2437 0.3212 REMARK 3 3 3.0562 - 2.6702 0.99 1271 148 0.2594 0.3343 REMARK 3 4 2.6702 - 2.4261 0.97 1242 139 0.3162 0.3916 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.29 REMARK 3 B_SOL : 19.33 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.360 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) : 1.94010 REMARK 3 B22 (A**2) : 4.56620 REMARK 3 B33 (A**2) : -5.46690 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 960 REMARK 3 ANGLE : 1.377 1272 REMARK 3 CHIRALITY : 0.088 150 REMARK 3 PLANARITY : 0.006 154 REMARK 3 DIHEDRAL : 13.951 392 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 61.4575 56.8640 9.0170 REMARK 3 T TENSOR REMARK 3 T11: 0.1738 T22: 0.2887 REMARK 3 T33: 0.1768 T12: 0.0037 REMARK 3 T13: -0.0101 T23: 0.0331 REMARK 3 L TENSOR REMARK 3 L11: 1.9536 L22: 1.1002 REMARK 3 L33: 1.2418 L12: -0.4658 REMARK 3 L13: -0.2144 L23: 0.1753 REMARK 3 S TENSOR REMARK 3 S11: -0.1041 S12: -0.0023 S13: -0.0502 REMARK 3 S21: 0.0104 S22: 0.0572 S23: 0.0982 REMARK 3 S31: -0.0512 S32: -0.0039 S33: 0.0483 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 1:61 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 1:61 ) REMARK 3 ATOM PAIRS NUMBER : 469 REMARK 3 RMSD : 0.063 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VTS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000095490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5614 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.426 REMARK 200 RESOLUTION RANGE LOW (A) : 30.112 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 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 <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: PHASER REMARK 200 STARTING MODEL: 1TGX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150MM AMMONIUM ACETATE, 100MM SODIUM REMARK 280 ACETATE, 25% POLYETHYLENE GLYCOL 4000 , PH 4.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 24.85900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.90650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.02850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.90650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.85900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.02850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 PHE A 10 -54.71 71.86 REMARK 500 PHE B 10 -53.63 71.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHOR DEPOSITED SEQUENCE OF THIS PROTEIN AS THE CODE B3EWH9 REMARK 999 BUT IT DOES NOT APPEAR IN TE SEQUENCE DATABASE YET. DBREF 3VTS A 1 61 PDB 3VTS 3VTS 1 61 DBREF 3VTS B 1 61 PDB 3VTS 3VTS 1 61 SEQRES 1 A 61 LEU LYS CYS HIS ASN LYS LEU VAL PRO PHE LEU SER LYS SEQRES 2 A 61 THR CYS PRO GLU GLY LYS ASN LEU CYS TYR LYS MET THR SEQRES 3 A 61 LEU MET LYS MET PRO LYS ILE PRO ILE LYS ARG GLY CYS SEQRES 4 A 61 THR ASP ALA CYS PRO LYS SER SER LEU LEU VAL LYS VAL SEQRES 5 A 61 VAL CYS CYS ASN LYS ASP LYS CYS ASN SEQRES 1 B 61 LEU LYS CYS HIS ASN LYS LEU VAL PRO PHE LEU SER LYS SEQRES 2 B 61 THR CYS PRO GLU GLY LYS ASN LEU CYS TYR LYS MET THR SEQRES 3 B 61 LEU MET LYS MET PRO LYS ILE PRO ILE LYS ARG GLY CYS SEQRES 4 B 61 THR ASP ALA CYS PRO LYS SER SER LEU LEU VAL LYS VAL SEQRES 5 B 61 VAL CYS CYS ASN LYS ASP LYS CYS ASN FORMUL 3 HOH *49(H2 O) SHEET 1 A 2 LYS A 2 HIS A 4 0 SHEET 2 A 2 SER A 12 THR A 14 -1 O LYS A 13 N CYS A 3 SHEET 1 B 3 MET A 30 THR A 40 0 SHEET 2 B 3 LEU A 21 LEU A 27 -1 N MET A 25 O ILE A 35 SHEET 3 B 3 VAL A 50 CYS A 55 -1 O CYS A 55 N CYS A 22 SHEET 1 C 2 LYS B 2 HIS B 4 0 SHEET 2 C 2 SER B 12 THR B 14 -1 O LYS B 13 N CYS B 3 SHEET 1 D 3 MET B 30 THR B 40 0 SHEET 2 D 3 LEU B 21 LEU B 27 -1 N MET B 25 O ILE B 35 SHEET 3 D 3 VAL B 50 CYS B 55 -1 O CYS B 55 N CYS B 22 SSBOND 1 CYS A 3 CYS A 22 1555 1555 2.04 SSBOND 2 CYS A 15 CYS A 39 1555 1555 2.04 SSBOND 3 CYS A 43 CYS A 54 1555 1555 2.03 SSBOND 4 CYS A 55 CYS A 60 1555 1555 2.05 SSBOND 5 CYS B 3 CYS B 22 1555 1555 2.02 SSBOND 6 CYS B 15 CYS B 39 1555 1555 2.04 SSBOND 7 CYS B 43 CYS B 54 1555 1555 2.04 SSBOND 8 CYS B 55 CYS B 60 1555 1555 2.02 CRYST1 49.718 50.057 57.813 90.00 90.00 90.00 P 21 21 21 8 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 0.020113 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017297 0.00000