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 3 27-DEC-23 4LFS 1 LINK 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 DEV_1313 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) : 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 DEPOSITION ID IS D_1000080574. 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 : SCALEPACK, 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 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