HEADER TOXIN 27-JUN-13 4LFS TITLE HIGH RESOLUTION X-RAY STRUCTURE OF RACEMIC SHK TOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POTASSIUM CHANNEL TOXIN SHK; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STICHODACTYLA HELIANTHUS; SOURCE 4 ORGANISM_COMMON: CARRIBEAN SEA ANEMONE; SOURCE 5 ORGANISM_TAXID: 6123; SOURCE 6 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS SHK TOXIN, CHEMICAL PROTEIN SYNTHESIS, RACEMIC PROTEIN KEYWDS 2 CRYSTALLOGRAPHY, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR B.DANG,T.KUBOTA,K.MANDAL,F.BEZANILLA,S.B.H.KENT REVDAT 2 04-SEP-13 4LFS 1 JRNL REVDAT 1 14-AUG-13 4LFS 0 JRNL AUTH B.DANG,T.KUBOTA,K.MANDAL,F.BEZANILLA,S.B.KENT JRNL TITL NATIVE CHEMICAL LIGATION AT ASX-CYS, GLX-CYS: CHEMICAL JRNL TITL 2 SYNTHESIS AND HIGH-RESOLUTION X-RAY STRUCTURE OF SHK TOXIN JRNL TITL 3 BY RACEMIC PROTEIN CRYSTALLOGRAPHY. JRNL REF J.AM.CHEM.SOC. V. 135 11911 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23919482 JRNL DOI 10.1021/JA4046795 REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1313) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 35303 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1753 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 25.8357 - 2.2793 0.95 2589 150 0.1909 0.1986 REMARK 3 2 2.2793 - 1.8093 0.97 2643 139 0.1505 0.1724 REMARK 3 3 1.8093 - 1.5806 0.96 2641 134 0.1330 0.1311 REMARK 3 4 1.5806 - 1.4361 0.97 2663 129 0.1190 0.1277 REMARK 3 5 1.4361 - 1.3332 0.97 2644 144 0.1183 0.1362 REMARK 3 6 1.3332 - 1.2546 0.94 2576 126 0.1116 0.1229 REMARK 3 7 1.2546 - 1.1917 0.96 2633 127 0.1136 0.1528 REMARK 3 8 1.1917 - 1.1399 0.95 2608 142 0.1125 0.1235 REMARK 3 9 1.1399 - 1.0960 0.93 2545 135 0.1197 0.1279 REMARK 3 10 1.0960 - 1.0582 0.94 2539 155 0.1373 0.1624 REMARK 3 11 1.0582 - 1.0251 0.92 2547 143 0.1417 0.1542 REMARK 3 12 1.0251 - 0.9958 0.93 2517 134 0.1489 0.1564 REMARK 3 13 0.9958 - 0.9696 0.87 2405 95 0.1591 0.1772 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.040 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.36 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 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 : 0.007 326 REMARK 3 ANGLE : 1.416 430 REMARK 3 CHIRALITY : 0.076 45 REMARK 3 PLANARITY : 0.006 53 REMARK 3 DIHEDRAL : 11.055 134 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: NULL REMARK 4 REMARK 4 4LFS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-13. REMARK 100 THE RCSB ID CODE IS RCSB080574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.688 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35825 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M TRIS, PH 8.5, 25 % POLYETHYLENE GLYCOL 3,350, 20 MM NACL , REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21/C 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+1/2 REMARK 290 3555 -X,-Y,-Z REMARK 290 4555 X,-Y+1/2,Z+1/2 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 -2.63891 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.82650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 10.19655 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 -2.63891 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.82650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 10.19655 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LFQ RELATED DB: PDB DBREF 4LFS A 1 35 UNP P29187 TXSHK_STOHE 1 35 SEQRES 1 A 35 ARG SER CYS ILE ASP THR ILE PRO LYS SER ARG CYS THR SEQRES 2 A 35 ALA PHE GLN CYS LYS HIS SER MET LYS TYR ARG LEU SER SEQRES 3 A 35 PHE CYS ARG LYS THR CYS GLY THR CYS HET CL A 101 2 HET CL A 102 2 HET CL A 103 2 HET GOL A 104 14 HET CL A 105 2 HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CL 4(CL 1-) FORMUL 5 GOL C3 H8 O3 FORMUL 7 HOH *75(H2 O) HELIX 1 1 PRO A 8 CYS A 12 5 5 HELIX 2 2 THR A 13 SER A 20 1 8 HELIX 3 3 SER A 20 SER A 26 1 7 SSBOND 1 CYS A 3 CYS A 35 1555 1555 2.04 SSBOND 2 CYS A 12 CYS A 28 1555 1555 2.05 SSBOND 3 CYS A 17 CYS A 32 1555 1555 2.03 LINK SG CYS A 17 SG CYS A 32 1555 1555 2.03 LINK SG CYS A 3 SG CYS A 35 1555 1555 2.04 LINK SG CYS A 12 SG CYS A 28 1555 1555 2.05 CRYST1 30.912 51.653 21.065 90.00 104.51 90.00 P 1 21/C 1 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 0.032350 0.000000 0.008372 0.00000 SCALE2 0.000000 0.019360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.049036 0.00000 MASTER 205 0 5 3 0 0 0 6 0 0 0 3 END