HEADER TOXIN 18-NOV-14 4RUD TITLE CRYSTAL STRUCTURE OF A THREE FINGER TOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THREE-FINGER TOXIN 3B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 22-79; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MICRURUS FULVIUS; SOURCE 3 ORGANISM_COMMON: HARLEQUIN CORALSNAKE; SOURCE 4 ORGANISM_TAXID: 8637; SOURCE 5 EXPRESSION_SYSTEM: XENOPUS LAEVIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 8355; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: OOCYTES KEYWDS THREE FINGER TOXIN, SNAKE VENOM TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR C.JOBICHEN,J.SIVARAMAN REVDAT 6 08-NOV-23 4RUD 1 REMARK REVDAT 5 24-AUG-22 4RUD 1 JRNL REMARK REVDAT 4 22-JAN-20 4RUD 1 COMPND SOURCE JRNL REVDAT 3 18-JUL-18 4RUD 1 SEQADV REVDAT 2 22-NOV-17 4RUD 1 REMARK REVDAT 1 18-MAY-16 4RUD 0 JRNL AUTH C.S.FOO,C.JOBICHEN,V.HASSAN-PUTTASWAMY,Z.DEKAN,H.S.TAE, JRNL AUTH 2 D.BERTRAND,D.J.ADAMS,P.F.ALEWOOD,J.SIVARAMAN,S.NIRTHANAN, JRNL AUTH 3 R.M.KINI JRNL TITL FULDITOXIN, REPRESENTING A NEW CLASS OF DIMERIC SNAKE JRNL TITL 2 TOXINS, DEFINES NOVEL PHARMACOLOGY AT NICOTINIC ACH JRNL TITL 3 RECEPTORS. JRNL REF BR.J.PHARMACOL. V. 177 1822 2020 JRNL REFN ISSN 0007-1188 JRNL PMID 31877243 JRNL DOI 10.1111/BPH.14954 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 17153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1705 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 30.2582 - 4.4600 1.00 1312 141 0.1904 0.2050 REMARK 3 2 4.4600 - 3.5418 1.00 1275 148 0.1589 0.1978 REMARK 3 3 3.5418 - 3.0946 1.00 1289 143 0.1780 0.2091 REMARK 3 4 3.0946 - 2.8119 1.00 1311 139 0.1930 0.2519 REMARK 3 5 2.8119 - 2.6105 1.00 1295 145 0.2025 0.2171 REMARK 3 6 2.6105 - 2.4566 1.00 1287 141 0.2126 0.2492 REMARK 3 7 2.4566 - 2.3337 1.00 1293 147 0.2264 0.2532 REMARK 3 8 2.3337 - 2.2321 0.97 1258 131 0.2991 0.3978 REMARK 3 9 2.2321 - 2.1462 0.97 1262 140 0.2587 0.2603 REMARK 3 10 2.1462 - 2.0722 1.00 1288 141 0.1814 0.2138 REMARK 3 11 2.0722 - 2.0074 1.00 1315 147 0.1832 0.2539 REMARK 3 12 2.0074 - 1.9500 1.00 1263 142 0.2446 0.3024 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 29.58 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.63670 REMARK 3 B22 (A**2) : -4.63670 REMARK 3 B33 (A**2) : 9.27340 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 : 0.007 932 REMARK 3 ANGLE : 1.244 1228 REMARK 3 CHIRALITY : 0.097 132 REMARK 3 PLANARITY : 0.004 154 REMARK 3 DIHEDRAL : 14.589 330 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 4RUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087806. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18858 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.255 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 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) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3PLC REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS-HCL, 150MM NACL, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 29.40000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.40000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.40000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.40000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.40000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.40000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.40000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 ZN ZN A 101 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN B 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 244 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 254 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 268 LIES ON A SPECIAL POSITION. 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 6 -169.13 -167.41 REMARK 500 LEU A 27 -71.07 -106.44 REMARK 500 ASN A 57 34.62 -86.09 REMARK 500 LEU B 27 -76.70 -105.63 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 ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 101 DBREF 4RUD A 1 58 UNP U3EPL2 U3EPL2_MICFL 22 79 DBREF 4RUD B 1 58 UNP U3EPL2 U3EPL2_MICFL 22 79 SEQADV 4RUD VAL A 25 UNP U3EPL2 ALA 46 CONFLICT SEQADV 4RUD VAL B 25 UNP U3EPL2 ALA 46 CONFLICT SEQRES 1 A 58 LEU LYS CYS TYR SER SER ARG THR GLU THR MET THR CYS SEQRES 2 A 58 PRO GLU GLY GLU ASP LYS CYS GLU LYS TYR ALA VAL GLY SEQRES 3 A 58 LEU MET HIS GLY SER PHE PHE PHE ILE TYR THR CYS THR SEQRES 4 A 58 SER LYS CYS HIS GLU GLY ALA TYR ASN VAL CYS CYS SER SEQRES 5 A 58 THR ASP LEU CYS ASN LYS SEQRES 1 B 58 LEU LYS CYS TYR SER SER ARG THR GLU THR MET THR CYS SEQRES 2 B 58 PRO GLU GLY GLU ASP LYS CYS GLU LYS TYR ALA VAL GLY SEQRES 3 B 58 LEU MET HIS GLY SER PHE PHE PHE ILE TYR THR CYS THR SEQRES 4 B 58 SER LYS CYS HIS GLU GLY ALA TYR ASN VAL CYS CYS SER SEQRES 5 B 58 THR ASP LEU CYS ASN LYS HET ZN A 101 1 HET ZN B 101 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *141(H2 O) SHEET 1 A 2 LYS A 2 TYR A 4 0 SHEET 2 A 2 THR A 10 THR A 12 -1 O MET A 11 N CYS A 3 SHEET 1 B 3 PHE A 32 THR A 39 0 SHEET 2 B 3 LYS A 19 GLY A 26 -1 N TYR A 23 O ILE A 35 SHEET 3 B 3 VAL A 49 CYS A 51 -1 O CYS A 51 N CYS A 20 SHEET 1 C 2 LYS B 2 TYR B 4 0 SHEET 2 C 2 THR B 10 THR B 12 -1 O MET B 11 N CYS B 3 SHEET 1 D 3 PHE B 32 THR B 39 0 SHEET 2 D 3 LYS B 19 GLY B 26 -1 N TYR B 23 O ILE B 35 SHEET 3 D 3 VAL B 49 CYS B 51 -1 O CYS B 51 N CYS B 20 SSBOND 1 CYS A 3 CYS A 20 1555 1555 2.04 SSBOND 2 CYS A 13 CYS A 38 1555 1555 2.03 SSBOND 3 CYS A 42 CYS A 50 1555 1555 2.01 SSBOND 4 CYS A 51 CYS A 56 1555 1555 2.03 SSBOND 5 CYS B 3 CYS B 20 1555 1555 2.01 SSBOND 6 CYS B 13 CYS B 38 1555 1555 2.05 SSBOND 7 CYS B 42 CYS B 50 1555 1555 2.02 SSBOND 8 CYS B 51 CYS B 56 1555 1555 2.03 LINK NE2 HIS A 29 ZN ZN A 101 1555 1555 2.05 LINK NE2 HIS B 29 ZN ZN B 101 1555 1555 2.06 SITE 1 AC1 2 HIS A 29 HOH A 254 SITE 1 AC2 1 HIS B 29 CRYST1 58.800 58.800 70.567 90.00 90.00 90.00 P 4 21 2 16 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 0.017007 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014171 0.00000