HEADER OXIDOREDUCTASE 29-JUN-20 6XM8 TITLE CRYSTAL STRUCTURE OF LIGNOSTILBENE BOUND TO CO-LSD4 FROM SPHINGOBIUM TITLE 2 SP. STRAIN SYK-6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LSD4; COMPND 5 EC: 1.13.11.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPHINGOBIUM SP. (STRAIN NBRC 103272 / SYK-6); SOURCE 3 ORGANISM_TAXID: 627192; SOURCE 4 STRAIN: NBRC 103272 / SYK-6; SOURCE 5 GENE: SLG_12860; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGNOSTILBENE DIOXYGENASE, CAROTENOID CLEAVAGE DIOXYGENASE, NON-HEME KEYWDS 2 IRON OXYGENASE, BACTERIAL AROMATIC CATABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR E.KUATSJAH,A.C.CHAN,R.KATAHIRA,G.T.BECKHAM,M.E.MURPHY,L.D.ELTIS REVDAT 4 18-OCT-23 6XM8 1 REMARK REVDAT 3 21-JUL-21 6XM8 1 JRNL REVDAT 2 26-MAY-21 6XM8 1 JRNL REVDAT 1 12-MAY-21 6XM8 0 JRNL AUTH E.KUATSJAH,A.C.K.CHAN,R.KATAHIRA,S.J.HAUGEN,G.T.BECKHAM, JRNL AUTH 2 M.E.P.MURPHY,L.D.ELTIS JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF LIGNOSTILBENE JRNL TITL 2 DIOXYGENASES FROM SPHINGOBIUM SP. SYK-6. JRNL REF J.BIOL.CHEM. V. 296 00758 2021 JRNL REFN ESSN 1083-351X JRNL PMID 33965373 JRNL DOI 10.1016/J.JBC.2021.100758 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14-3260 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 92137 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 4601 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 40.3050 - 5.7430 0.99 2892 154 0.1852 0.2163 REMARK 3 2 5.7430 - 4.5604 1.00 2917 154 0.1267 0.1329 REMARK 3 3 4.5604 - 3.9845 1.00 2909 155 0.1090 0.1093 REMARK 3 4 3.9845 - 3.6205 1.00 2949 154 0.1195 0.1437 REMARK 3 5 3.6205 - 3.3611 1.00 2920 153 0.1292 0.1751 REMARK 3 6 3.3611 - 3.1630 1.00 2904 151 0.1320 0.1726 REMARK 3 7 3.1630 - 3.0047 1.00 2951 151 0.1409 0.1512 REMARK 3 8 3.0047 - 2.8739 1.00 2888 155 0.1365 0.1670 REMARK 3 9 2.8739 - 2.7633 1.00 2888 154 0.1321 0.1599 REMARK 3 10 2.7633 - 2.6680 1.00 2959 156 0.1384 0.1669 REMARK 3 11 2.6680 - 2.5846 1.00 2925 157 0.1351 0.1921 REMARK 3 12 2.5846 - 2.5107 1.00 2915 153 0.1343 0.1663 REMARK 3 13 2.5107 - 2.4446 1.00 2885 157 0.1347 0.1449 REMARK 3 14 2.4446 - 2.3850 1.00 2942 152 0.1326 0.1565 REMARK 3 15 2.3850 - 2.3308 1.00 2914 150 0.1318 0.1965 REMARK 3 16 2.3308 - 2.2812 1.00 2890 150 0.1344 0.1608 REMARK 3 17 2.2812 - 2.2355 1.00 2952 155 0.1401 0.1550 REMARK 3 18 2.2355 - 2.1933 1.00 2950 155 0.1451 0.1675 REMARK 3 19 2.1933 - 2.1542 1.00 2899 154 0.1492 0.1622 REMARK 3 20 2.1542 - 2.1177 1.00 2903 153 0.1562 0.1647 REMARK 3 21 2.1177 - 2.0835 1.00 2871 151 0.1576 0.1859 REMARK 3 22 2.0835 - 2.0515 1.00 2975 158 0.1661 0.2042 REMARK 3 23 2.0515 - 2.0213 1.00 2890 150 0.1704 0.2169 REMARK 3 24 2.0213 - 1.9928 1.00 2874 150 0.1804 0.2053 REMARK 3 25 1.9928 - 1.9659 1.00 3009 160 0.1852 0.2370 REMARK 3 26 1.9659 - 1.9404 1.00 2854 150 0.1945 0.2382 REMARK 3 27 1.9404 - 1.9161 1.00 2964 154 0.2126 0.2624 REMARK 3 28 1.9161 - 1.8930 1.00 2882 152 0.2319 0.2252 REMARK 3 29 1.8930 - 1.8710 1.00 2929 149 0.2440 0.2747 REMARK 3 30 1.8710 - 1.8500 1.00 2936 154 0.2770 0.3430 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.87 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 237 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9761 9.6973 38.5286 REMARK 3 T TENSOR REMARK 3 T11: 0.0919 T22: 0.1091 REMARK 3 T33: 0.1043 T12: -0.0051 REMARK 3 T13: -0.0064 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.1868 L22: 0.4673 REMARK 3 L33: 0.3093 L12: 0.0346 REMARK 3 L13: 0.0247 L23: -0.1387 REMARK 3 S TENSOR REMARK 3 S11: 0.0027 S12: 0.0147 S13: 0.0032 REMARK 3 S21: -0.0691 S22: 0.0062 S23: 0.0489 REMARK 3 S31: 0.0355 S32: -0.0269 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 238 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6132 18.1268 19.6743 REMARK 3 T TENSOR REMARK 3 T11: 0.1962 T22: 0.1530 REMARK 3 T33: 0.1332 T12: -0.0022 REMARK 3 T13: 0.0113 T23: 0.0270 REMARK 3 L TENSOR REMARK 3 L11: 0.0728 L22: 0.0779 REMARK 3 L33: 0.0976 L12: 0.0757 REMARK 3 L13: 0.0314 L23: -0.0445 REMARK 3 S TENSOR REMARK 3 S11: -0.0310 S12: 0.1142 S13: 0.0186 REMARK 3 S21: -0.2697 S22: 0.0337 S23: 0.0265 REMARK 3 S31: 0.0415 S32: -0.0171 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 333 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.0182 21.3121 29.2739 REMARK 3 T TENSOR REMARK 3 T11: 0.1332 T22: 0.1355 REMARK 3 T33: 0.1540 T12: -0.0028 REMARK 3 T13: 0.0239 T23: 0.0282 REMARK 3 L TENSOR REMARK 3 L11: 0.0332 L22: 0.0714 REMARK 3 L33: 0.1459 L12: 0.0650 REMARK 3 L13: -0.0203 L23: 0.0100 REMARK 3 S TENSOR REMARK 3 S11: 0.0063 S12: 0.0253 S13: 0.0041 REMARK 3 S21: -0.0653 S22: -0.0489 S23: -0.1305 REMARK 3 S31: -0.0764 S32: 0.0620 S33: -0.0274 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 334 THROUGH 373 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0505 29.7241 35.4392 REMARK 3 T TENSOR REMARK 3 T11: 0.1457 T22: 0.1457 REMARK 3 T33: 0.1357 T12: -0.0202 REMARK 3 T13: 0.0099 T23: 0.0247 REMARK 3 L TENSOR REMARK 3 L11: -0.0009 L22: 0.0667 REMARK 3 L33: 0.0416 L12: 0.0314 REMARK 3 L13: 0.0578 L23: 0.0017 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: -0.0103 S13: 0.0021 REMARK 3 S21: -0.0177 S22: -0.0371 S23: -0.0027 REMARK 3 S31: -0.1259 S32: 0.0790 S33: -0.0182 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 374 THROUGH 404 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.4048 21.1166 45.4893 REMARK 3 T TENSOR REMARK 3 T11: 0.1210 T22: 0.1860 REMARK 3 T33: 0.2238 T12: -0.0408 REMARK 3 T13: 0.0106 T23: 0.0473 REMARK 3 L TENSOR REMARK 3 L11: 0.0740 L22: 0.1649 REMARK 3 L33: 0.1370 L12: -0.0751 REMARK 3 L13: -0.0152 L23: 0.0788 REMARK 3 S TENSOR REMARK 3 S11: -0.0071 S12: 0.0718 S13: 0.0046 REMARK 3 S21: -0.1611 S22: -0.0399 S23: -0.1856 REMARK 3 S31: -0.0908 S32: 0.1422 S33: 0.0009 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 405 THROUGH 489 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.6388 19.1074 53.4323 REMARK 3 T TENSOR REMARK 3 T11: 0.1049 T22: 0.1167 REMARK 3 T33: 0.1227 T12: -0.0225 REMARK 3 T13: -0.0072 T23: 0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.0982 L22: 0.1166 REMARK 3 L33: 0.2301 L12: 0.0904 REMARK 3 L13: -0.0770 L23: -0.1517 REMARK 3 S TENSOR REMARK 3 S11: 0.0240 S12: -0.0254 S13: 0.0231 REMARK 3 S21: 0.0665 S22: -0.0536 S23: -0.0156 REMARK 3 S31: -0.0622 S32: 0.0391 S33: -0.0385 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 6XM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000250144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92163 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 40.305 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.819 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.79 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 6OJR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M MAGNESIUM ACETATE, 29% PEG3350, REMARK 280 PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 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 -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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 42.85000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.27000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.76000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.85000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.27000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.76000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.85000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.27000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.76000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.85000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.27000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.76000 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 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 115.52000 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 HOH A 740 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1070 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1140 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 LYS A 383 REMARK 465 GLY A 384 REMARK 465 GLY A 385 REMARK 465 SER A 386 REMARK 465 ALA A 387 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 ASP A 46 108.95 -160.99 REMARK 500 PHE A 310 75.98 -118.38 REMARK 500 GLU A 381 41.39 -96.70 REMARK 500 LEU A 475 -112.15 -106.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1277 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1278 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1279 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A1280 DISTANCE = 7.03 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 501 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 167 NE2 REMARK 620 2 HIS A 218 NE2 95.3 REMARK 620 3 HIS A 284 NE2 104.4 104.8 REMARK 620 4 HIS A 476 NE2 94.1 147.9 102.4 REMARK 620 5 HOH A 749 O 163.5 79.4 92.1 82.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 508 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 854 O REMARK 620 2 HOH A 983 O 99.8 REMARK 620 3 HOH A1061 O 93.2 84.9 REMARK 620 4 HOH A1121 O 167.0 77.3 99.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V5P A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 508 DBREF 6XM8 A 1 489 UNP G2IQT9 G2IQT9_SPHSK 1 489 SEQRES 1 A 489 MET ALA HIS PHE PRO ASP THR PRO ALA PHE THR GLY PHE SEQRES 2 A 489 ASN ALA PRO SER ARG ILE GLU CYS ASP ILE PRO ASN LEU SEQRES 3 A 489 VAL HIS GLU GLY THR ILE PRO PRO GLU LEU ASN GLY ALA SEQRES 4 A 489 PHE PHE ARG VAL GLN PRO ASP PRO GLN PHE PRO PRO ARG SEQRES 5 A 489 LEU GLY ASP ASP ILE SER PHE ASN GLY ASP GLY MET ILE SEQRES 6 A 489 THR ARG PHE HIS ILE HIS ASP GLY GLN CYS ASP ILE LYS SEQRES 7 A 489 GLN ARG TRP ALA LYS THR ASN LYS TRP LYS LEU GLU ASN SEQRES 8 A 489 ALA ALA GLY LYS ALA LEU PHE GLY SER TYR ARG ASN PRO SEQRES 9 A 489 LEU THR ASP ASP GLU SER VAL LYS GLY GLU TYR ARG SER SEQRES 10 A 489 THR ALA ASN THR ASN ALA PHE VAL PHE ALA GLY LYS LEU SEQRES 11 A 489 TRP ALA MET LYS GLU ASP SER PRO SER LEU THR MET ASP SEQRES 12 A 489 PRO ALA THR MET GLU THR PHE GLY PHE GLU LYS PHE GLY SEQRES 13 A 489 GLY LYS MET THR GLY GLN THR PHE THR ALA HIS PRO LYS SEQRES 14 A 489 VAL ASP PRO LEU THR GLY ASN MET VAL ALA ILE GLY TYR SEQRES 15 A 489 ALA ALA SER GLY LEU CYS THR ASP ASP VAL CYS LEU TYR SEQRES 16 A 489 GLU ILE SER PRO ASP GLY GLU LEU ILE TYR GLU ALA TRP SEQRES 17 A 489 PHE LYS VAL PRO TYR TYR CYS MET MET HIS ASP PHE GLY SEQRES 18 A 489 VAL THR LYS ASP TYR LEU VAL LEU HIS ILE VAL PRO SER SEQRES 19 A 489 ILE GLY SER TRP ASP ARG LEU GLU LYS GLY LEU PRO HIS SEQRES 20 A 489 PHE GLY PHE ASP THR THR LEU PRO VAL TYR LEU GLY ILE SEQRES 21 A 489 ILE PRO ARG ARG ALA ASP LEU LYS GLN GLU ASP ILE ARG SEQRES 22 A 489 TRP PHE LYS ARG GLU ASN CYS PHE ALA SER HIS VAL MET SEQRES 23 A 489 ASN ALA PHE GLN GLU GLY THR LYS VAL HIS VAL ASP VAL SEQRES 24 A 489 PRO GLU ALA GLU ASN ASN MET PHE PRO PHE PHE PRO ASP SEQRES 25 A 489 VAL HIS GLY ALA PRO PHE ASN PRO GLN GLN ALA MET SER SEQRES 26 A 489 ARG LEU THR ARG TRP THR VAL ASP MET ALA SER ASN SER SEQRES 27 A 489 ASP GLU PHE ASP SER VAL THR ARG LEU THR GLU THR ALA SEQRES 28 A 489 GLY GLU PHE PRO ARG ILE ASP ASP ARG MET THR GLY LEU SEQRES 29 A 489 PRO TYR ARG TYR GLY TRP MET LEU GLU MET ASP MET LYS SEQRES 30 A 489 ARG PRO VAL GLU LEU LYS GLY GLY SER ALA GLY GLY PHE SEQRES 31 A 489 LEU MET ASN CYS LEU PHE LEU LYS ASP HIS GLN THR GLY SEQRES 32 A 489 ALA GLU GLN HIS TRP TRP CYS GLY PRO THR SER SER LEU SEQRES 33 A 489 GLN GLU PRO ALA PHE ILE PRO ARG SER LYS ASP ALA PRO SEQRES 34 A 489 GLU GLY ASP GLY TRP ILE VAL GLN VAL CYS ASN ARG LEU SEQRES 35 A 489 ALA ASP HIS LYS SER ASP LEU LEU ILE PHE GLU ALA LEU SEQRES 36 A 489 ASP ILE GLU LYS GLY PRO VAL ALA THR VAL HIS LEU PRO SEQRES 37 A 489 PHE ALA LEU ARG PHE GLY LEU HIS GLY ASN TRP ALA ASN SEQRES 38 A 489 ALA GLU GLU ILE GLY LEU ALA ALA HET CO A 501 1 HET V5P A 502 36 HET DMS A 503 10 HET DMS A 504 10 HET DMS A 505 10 HET DMS A 506 10 HET DMS A 507 10 HET MG A 508 1 HETNAM CO COBALT (II) ION HETNAM V5P LIGNOSTILBENE HETNAM DMS DIMETHYL SULFOXIDE HETNAM MG MAGNESIUM ION HETSYN V5P 4,4'-[(E)-ETHENE-1,2-DIYL]BIS(2-METHOXYPHENOL) FORMUL 2 CO CO 2+ FORMUL 3 V5P C16 H16 O4 FORMUL 4 DMS 5(C2 H6 O S) FORMUL 9 MG MG 2+ FORMUL 10 HOH *680(H2 O) HELIX 1 AA1 THR A 7 ALA A 15 5 9 HELIX 2 AA2 ILE A 57 GLY A 61 5 5 HELIX 3 AA3 THR A 84 GLY A 94 1 11 HELIX 4 AA4 ASN A 103 ASP A 107 5 5 HELIX 5 AA5 ASP A 108 LYS A 112 5 5 HELIX 6 AA6 LYS A 154 LYS A 158 5 5 HELIX 7 AA7 SER A 237 LYS A 243 1 7 HELIX 8 AA8 LYS A 268 ILE A 272 5 5 HELIX 9 AA9 PRO A 320 MET A 324 5 5 HELIX 10 AB1 ASP A 358 THR A 362 5 5 HELIX 11 AB2 GLU A 483 ILE A 485 5 3 SHEET 1 AA1 5 CYS A 21 ILE A 23 0 SHEET 2 AA1 5 GLN A 74 TRP A 81 -1 O ILE A 77 N ILE A 23 SHEET 3 AA1 5 GLY A 63 HIS A 71 -1 N ILE A 65 O ARG A 80 SHEET 4 AA1 5 GLY A 38 PRO A 45 -1 N PHE A 40 O PHE A 68 SHEET 5 AA1 5 GLY A 477 ASN A 481 -1 O ASN A 478 N PHE A 41 SHEET 1 AA2 5 HIS A 28 GLY A 30 0 SHEET 2 AA2 5 ALA A 463 HIS A 466 -1 O THR A 464 N GLU A 29 SHEET 3 AA2 5 LYS A 446 GLU A 453 -1 N LEU A 449 O VAL A 465 SHEET 4 AA2 5 GLY A 433 ARG A 441 -1 N ILE A 435 O PHE A 452 SHEET 5 AA2 5 SER A 414 LEU A 416 -1 N SER A 415 O ASN A 440 SHEET 1 AA3 5 HIS A 28 GLY A 30 0 SHEET 2 AA3 5 ALA A 463 HIS A 466 -1 O THR A 464 N GLU A 29 SHEET 3 AA3 5 LYS A 446 GLU A 453 -1 N LEU A 449 O VAL A 465 SHEET 4 AA3 5 GLY A 433 ARG A 441 -1 N ILE A 435 O PHE A 452 SHEET 5 AA3 5 ALA A 420 PRO A 423 -1 N ILE A 422 O TRP A 434 SHEET 1 AA4 4 ASN A 122 PHE A 126 0 SHEET 2 AA4 4 LYS A 129 MET A 133 -1 O TRP A 131 N PHE A 124 SHEET 3 AA4 4 LEU A 140 MET A 142 -1 O MET A 142 N LEU A 130 SHEET 4 AA4 4 THR A 149 PHE A 152 -1 O PHE A 150 N THR A 141 SHEET 1 AA5 4 LYS A 169 VAL A 170 0 SHEET 2 AA5 4 MET A 177 TYR A 182 -1 O VAL A 178 N LYS A 169 SHEET 3 AA5 4 ASP A 191 ILE A 197 -1 O TYR A 195 N ALA A 179 SHEET 4 AA5 4 LEU A 203 LYS A 210 -1 O PHE A 209 N VAL A 192 SHEET 1 AA6 4 GLY A 221 VAL A 222 0 SHEET 2 AA6 4 TYR A 226 ILE A 231 -1 O VAL A 228 N GLY A 221 SHEET 3 AA6 4 VAL A 256 PRO A 262 -1 O ILE A 261 N LEU A 227 SHEET 4 AA6 4 ARG A 273 ARG A 277 -1 O ARG A 277 N VAL A 256 SHEET 1 AA7 2 SER A 234 GLY A 236 0 SHEET 2 AA7 2 PHE A 248 PHE A 250 -1 O GLY A 249 N ILE A 235 SHEET 1 AA8 3 PHE A 281 ALA A 282 0 SHEET 2 AA8 3 LYS A 294 ALA A 302 -1 O ALA A 302 N PHE A 281 SHEET 3 AA8 3 ASN A 287 GLU A 291 -1 N PHE A 289 O HIS A 296 SHEET 1 AA9 7 PHE A 281 ALA A 282 0 SHEET 2 AA9 7 LYS A 294 ALA A 302 -1 O ALA A 302 N PHE A 281 SHEET 3 AA9 7 ARG A 326 ASP A 333 -1 O TRP A 330 N VAL A 297 SHEET 4 AA9 7 SER A 343 ARG A 356 -1 O THR A 345 N ARG A 329 SHEET 5 AA9 7 TYR A 368 GLU A 373 -1 O TRP A 370 N ARG A 356 SHEET 6 AA9 7 CYS A 394 ASP A 399 -1 O CYS A 394 N GLU A 373 SHEET 7 AA9 7 GLU A 405 TRP A 409 -1 O TRP A 408 N LEU A 395 LINK NE2 HIS A 167 CO CO A 501 1555 1555 2.06 LINK NE2 HIS A 218 CO CO A 501 1555 1555 2.07 LINK NE2 HIS A 284 CO CO A 501 1555 1555 2.04 LINK NE2 HIS A 476 CO CO A 501 1555 1555 2.02 LINK CO CO A 501 O HOH A 749 1555 1555 2.19 LINK MG MG A 508 O HOH A 854 1555 1555 1.90 LINK MG MG A 508 O HOH A 983 1555 1555 2.13 LINK MG MG A 508 O HOH A1061 1555 1555 2.04 LINK MG MG A 508 O HOH A1121 1555 1555 2.09 SITE 1 AC1 5 HIS A 167 HIS A 218 HIS A 284 HIS A 476 SITE 2 AC1 5 HOH A 749 SITE 1 AC2 12 PHE A 59 TYR A 101 ASN A 120 THR A 121 SITE 2 AC2 12 LYS A 134 MET A 216 HIS A 218 HIS A 284 SITE 3 AC2 12 GLU A 353 PHE A 354 LEU A 475 HOH A 749 SITE 1 AC3 5 ASP A 55 ASP A 56 ILE A 57 HOH A 641 SITE 2 AC3 5 HOH A 890 SITE 1 AC4 8 GLU A 35 LEU A 36 ASN A 37 PRO A 423 SITE 2 AC4 8 TRP A 434 TRP A 479 ASN A 481 HOH A 789 SITE 1 AC5 5 MET A 361 ALA A 428 GLU A 430 HOH A 610 SITE 2 AC5 5 HOH A 671 SITE 1 AC6 5 GLY A 113 GLU A 114 GLN A 162 HOH A 858 SITE 2 AC6 5 HOH A1018 SITE 1 AC7 6 GLU A 29 GLY A 30 PRO A 461 VAL A 462 SITE 2 AC7 6 ALA A 463 THR A 464 SITE 1 AC8 4 HOH A 854 HOH A 983 HOH A1061 HOH A1121 CRYST1 85.700 112.540 115.520 90.00 90.00 90.00 I 2 2 2 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 0.011669 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008657 0.00000