HEADER UNKNOWN FUNCTION 16-MAY-23 8P2U TITLE CRYSTAL STRUCTURE OF S6BE WITH SILICOTUNGSTIC ACID (STA) TITLE 2 POLYOXOMETALATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: S6BE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA PROPELLER, SYNTHETIC, DESIGNER, POLYOXOMETALATE, STA, CO- KEYWDS 2 CRYSTAL, SILICOTUNGSTIC ACID, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.M.L.WOUTERS,K.KAMATA,L.VANDEBROEK REVDAT 1 12-JUN-24 8P2U 0 JRNL AUTH S.M.L.WOUTERS,K.KAMATA,K.TAKAHASHI,L.VANDEBROEK, JRNL AUTH 2 T.N.PARAC-VOGT,J.R.H.TAME,A.R.D.VOET JRNL TITL CRYSTAL STRUCTURE OF S6BE WITH SILICOTUNGSTIC ACID (STA) JRNL TITL 2 POLYOXOMETALATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2-4158 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 76.5 REMARK 3 NUMBER OF REFLECTIONS : 61953 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3132 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 38.3800 - 3.9200 0.84 2954 131 0.1758 0.1815 REMARK 3 2 3.9200 - 3.1100 0.84 2973 159 0.1563 0.2042 REMARK 3 3 3.1100 - 2.7200 0.79 2716 148 0.1644 0.1941 REMARK 3 4 2.7200 - 2.4700 0.82 2922 172 0.1674 0.1805 REMARK 3 5 2.4700 - 2.2900 0.76 2603 148 0.1679 0.1954 REMARK 3 6 2.2900 - 2.1600 0.80 2752 175 0.1549 0.1979 REMARK 3 7 2.1600 - 2.0500 0.81 2858 160 0.1505 0.1535 REMARK 3 8 2.0500 - 1.9600 0.78 2693 155 0.1483 0.1983 REMARK 3 9 1.9600 - 1.8900 0.75 2605 163 0.1587 0.2393 REMARK 3 10 1.8900 - 1.8200 0.78 2720 134 0.1818 0.1815 REMARK 3 11 1.8200 - 1.7600 0.76 2646 122 0.1886 0.2248 REMARK 3 12 1.7600 - 1.7100 0.73 2643 112 0.1959 0.2035 REMARK 3 13 1.7100 - 1.6700 0.77 2709 133 0.2046 0.2760 REMARK 3 14 1.6700 - 1.6300 0.76 2713 119 0.2177 0.3002 REMARK 3 15 1.6300 - 1.5900 0.77 2645 145 0.2199 0.2612 REMARK 3 16 1.5900 - 1.5600 0.73 2617 106 0.2201 0.2491 REMARK 3 17 1.5600 - 1.5300 0.71 2446 137 0.2314 0.2968 REMARK 3 18 1.5300 - 1.5000 0.73 2574 126 0.2368 0.2914 REMARK 3 19 1.5000 - 1.4700 0.75 2632 161 0.2509 0.3122 REMARK 3 20 1.4700 - 1.4500 0.68 2340 136 0.2310 0.3221 REMARK 3 21 1.4500 - 1.4200 0.72 2510 177 0.2416 0.2527 REMARK 3 22 1.4200 - 1.4000 0.74 2550 113 0.2435 0.2754 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.670 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) : 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 2289 REMARK 3 ANGLE : 1.446 3342 REMARK 3 CHIRALITY : 0.094 337 REMARK 3 PLANARITY : 0.013 390 REMARK 3 DIHEDRAL : 10.321 813 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 8P2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130556. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61953 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 38.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.13400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M SODIUM MALONATE, PH 5.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 MET A 21 REMARK 465 ASN A 22 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 GLU A 49 CG CD OE1 OE2 REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 ARG A 94 CD NE CZ NH1 NH2 REMARK 470 GLU A 143 CG CD OE1 OE2 REMARK 470 GLU A 187 CD OE1 OE2 REMARK 470 ARG A 188 NE CZ NH1 NH2 REMARK 470 GLU A 190 CD OE1 OE2 REMARK 470 GLU A 234 CG CD OE1 OE2 REMARK 470 ARG A 235 CD NE CZ NH1 NH2 REMARK 470 GLU A 284 CG CD OE1 OE2 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 VAL A 53 -163.97 -111.44 REMARK 500 VAL A 100 -164.48 -119.37 REMARK 500 VAL A 147 -164.63 -118.49 REMARK 500 VAL A 194 -164.37 -113.08 REMARK 500 VAL A 241 -163.55 -117.76 REMARK 500 VAL A 288 -163.67 -118.25 REMARK 500 REMARK 500 REMARK: NULL DBREF 8P2U A 18 303 PDB 8P2U 8P2U 18 303 SEQRES 1 A 286 GLY SER HIS MET ASN GLY LEU ILE TYR ALA VAL GLY GLY SEQRES 2 A 286 TYR ASP GLY ASN THR HIS LEU ASN SER VAL GLU ALA TYR SEQRES 3 A 286 ASP PRO GLU ARG ASN GLU TRP SER LEU VAL ALA PRO LEU SEQRES 4 A 286 SER THR ARG ARG SER GLY VAL GLY VAL ALA VAL LEU ASN SEQRES 5 A 286 GLY LEU ILE TYR ALA VAL GLY GLY TYR ASP GLY ASN THR SEQRES 6 A 286 HIS LEU ASN SER VAL GLU ALA TYR ASP PRO GLU ARG ASN SEQRES 7 A 286 GLU TRP SER LEU VAL ALA PRO LEU SER THR ARG ARG SER SEQRES 8 A 286 GLY VAL GLY VAL ALA VAL LEU ASN GLY LEU ILE TYR ALA SEQRES 9 A 286 VAL GLY GLY TYR ASP GLY ASN THR HIS LEU ASN SER VAL SEQRES 10 A 286 GLU ALA TYR ASP PRO GLU ARG ASN GLU TRP SER LEU VAL SEQRES 11 A 286 ALA PRO LEU SER THR ARG ARG SER GLY VAL GLY VAL ALA SEQRES 12 A 286 VAL LEU ASN GLY LEU ILE TYR ALA VAL GLY GLY TYR ASP SEQRES 13 A 286 GLY ASN THR HIS LEU ASN SER VAL GLU ALA TYR ASP PRO SEQRES 14 A 286 GLU ARG ASN GLU TRP SER LEU VAL ALA PRO LEU SER THR SEQRES 15 A 286 ARG ARG SER GLY VAL GLY VAL ALA VAL LEU ASN GLY LEU SEQRES 16 A 286 ILE TYR ALA VAL GLY GLY TYR ASP GLY ASN THR HIS LEU SEQRES 17 A 286 ASN SER VAL GLU ALA TYR ASP PRO GLU ARG ASN GLU TRP SEQRES 18 A 286 SER LEU VAL ALA PRO LEU SER THR ARG ARG SER GLY VAL SEQRES 19 A 286 GLY VAL ALA VAL LEU ASN GLY LEU ILE TYR ALA VAL GLY SEQRES 20 A 286 GLY TYR ASP GLY ASN THR HIS LEU ASN SER VAL GLU ALA SEQRES 21 A 286 TYR ASP PRO GLU ARG ASN GLU TRP SER LEU VAL ALA PRO SEQRES 22 A 286 LEU SER THR ARG ARG SER GLY VAL GLY VAL ALA VAL LEU HET SIW A 401 106 HETNAM SIW KEGGIN (STA) FORMUL 2 SIW O40 SI W12 FORMUL 3 HOH *212(H2 O) SHEET 1 AA1 4 GLU A 49 LEU A 52 0 SHEET 2 AA1 4 HIS A 36 ASP A 44 -1 N ALA A 42 O SER A 51 SHEET 3 AA1 4 ILE A 25 TYR A 31 -1 N ILE A 25 O TYR A 43 SHEET 4 AA1 4 GLY A 299 VAL A 302 -1 O GLY A 299 N VAL A 28 SHEET 1 AA2 4 GLY A 64 LEU A 68 0 SHEET 2 AA2 4 LEU A 71 VAL A 75 -1 O TYR A 73 N ALA A 66 SHEET 3 AA2 4 VAL A 87 ASP A 91 -1 O GLU A 88 N ALA A 74 SHEET 4 AA2 4 GLU A 96 LEU A 99 -1 O SER A 98 N ALA A 89 SHEET 1 AA3 4 GLY A 111 LEU A 115 0 SHEET 2 AA3 4 LEU A 118 VAL A 122 -1 O VAL A 122 N GLY A 111 SHEET 3 AA3 4 VAL A 134 TYR A 137 -1 O GLU A 135 N ALA A 121 SHEET 4 AA3 4 TRP A 144 LEU A 146 -1 O SER A 145 N ALA A 136 SHEET 1 AA4 4 GLY A 158 LEU A 162 0 SHEET 2 AA4 4 LEU A 165 TYR A 172 -1 O VAL A 169 N GLY A 158 SHEET 3 AA4 4 HIS A 177 ASP A 185 -1 O TYR A 184 N ILE A 166 SHEET 4 AA4 4 GLU A 190 LEU A 193 -1 O SER A 192 N ALA A 183 SHEET 1 AA5 4 GLY A 205 LEU A 209 0 SHEET 2 AA5 4 LEU A 212 VAL A 216 -1 O TYR A 214 N ALA A 207 SHEET 3 AA5 4 VAL A 228 ASP A 232 -1 O GLU A 229 N ALA A 215 SHEET 4 AA5 4 GLU A 237 LEU A 240 -1 O SER A 239 N ALA A 230 SHEET 1 AA6 4 GLY A 252 LEU A 256 0 SHEET 2 AA6 4 LEU A 259 VAL A 263 -1 O VAL A 263 N GLY A 252 SHEET 3 AA6 4 VAL A 275 TYR A 278 -1 O GLU A 276 N ALA A 262 SHEET 4 AA6 4 TRP A 285 LEU A 287 -1 O SER A 286 N ALA A 277 CRYST1 34.976 43.244 44.069 63.28 90.00 66.15 P 1 1 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 0.028591 -0.012640 0.007136 0.00000 SCALE2 0.000000 0.025284 -0.014274 0.00000 SCALE3 0.000000 0.000000 0.026058 0.00000