HEADER OXIDOREDUCTASE 29-JUN-20 6XM6 TITLE CRYSTAL STRUCTURE OF COBALT-BOUND LSD4 FROM SPHINGOBIUM SP. STRAIN TITLE 2 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 6XM6 1 REMARK REVDAT 3 21-JUL-21 6XM6 1 JRNL REVDAT 2 26-MAY-21 6XM6 1 JRNL REVDAT 1 12-MAY-21 6XM6 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 188724 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 9407 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 43.8470 - 4.5038 1.00 5993 323 0.1416 0.1522 REMARK 3 2 4.5038 - 3.5753 1.00 5988 309 0.1094 0.1207 REMARK 3 3 3.5753 - 3.1235 1.00 5973 312 0.1259 0.1355 REMARK 3 4 3.1235 - 2.8380 1.00 5981 313 0.1296 0.1590 REMARK 3 5 2.8380 - 2.6346 1.00 6004 316 0.1193 0.1437 REMARK 3 6 2.6346 - 2.4793 1.00 5978 303 0.1176 0.1532 REMARK 3 7 2.4793 - 2.3551 1.00 5985 312 0.1168 0.1308 REMARK 3 8 2.3551 - 2.2526 1.00 6007 314 0.1217 0.1385 REMARK 3 9 2.2526 - 2.1659 1.00 5902 312 0.1113 0.1164 REMARK 3 10 2.1659 - 2.0911 1.00 6011 316 0.1156 0.1511 REMARK 3 11 2.0911 - 2.0258 1.00 6013 317 0.1243 0.1632 REMARK 3 12 2.0258 - 1.9678 1.00 5947 313 0.1313 0.1475 REMARK 3 13 1.9678 - 1.9160 1.00 6018 316 0.1347 0.1659 REMARK 3 14 1.9160 - 1.8693 1.00 5988 313 0.1409 0.1508 REMARK 3 15 1.8693 - 1.8268 1.00 5964 308 0.1354 0.1600 REMARK 3 16 1.8268 - 1.7879 1.00 5949 311 0.1390 0.1619 REMARK 3 17 1.7879 - 1.7522 1.00 6030 316 0.1304 0.1631 REMARK 3 18 1.7522 - 1.7191 1.00 5930 310 0.1348 0.1637 REMARK 3 19 1.7191 - 1.6884 1.00 5991 314 0.1272 0.1614 REMARK 3 20 1.6884 - 1.6598 1.00 5970 318 0.1303 0.1477 REMARK 3 21 1.6598 - 1.6330 1.00 6009 312 0.1296 0.1599 REMARK 3 22 1.6330 - 1.6079 1.00 5969 317 0.1339 0.1573 REMARK 3 23 1.6079 - 1.5842 1.00 5987 315 0.1493 0.1760 REMARK 3 24 1.5842 - 1.5619 1.00 5954 315 0.1756 0.1954 REMARK 3 25 1.5619 - 1.5408 1.00 5956 316 0.2023 0.2279 REMARK 3 26 1.5408 - 1.5208 1.00 6040 312 0.2467 0.2756 REMARK 3 27 1.5208 - 1.5018 1.00 5960 310 0.3144 0.3100 REMARK 3 28 1.5018 - 1.4837 0.99 5926 317 0.4285 0.3980 REMARK 3 29 1.4837 - 1.4664 0.99 5955 314 0.5487 0.5785 REMARK 3 30 1.4664 - 1.4500 1.00 5939 313 0.7218 0.8009 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.61 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 237 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9072 9.6086 38.1918 REMARK 3 T TENSOR REMARK 3 T11: 0.0929 T22: 0.1084 REMARK 3 T33: 0.0973 T12: 0.0002 REMARK 3 T13: -0.0011 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.1380 L22: 0.5250 REMARK 3 L33: 0.3073 L12: 0.1415 REMARK 3 L13: -0.0430 L23: -0.2696 REMARK 3 S TENSOR REMARK 3 S11: -0.0085 S12: 0.0082 S13: 0.0165 REMARK 3 S21: -0.0799 S22: 0.0249 S23: 0.0246 REMARK 3 S31: 0.0341 S32: -0.0260 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 238 THROUGH 333 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.4649 19.7832 24.8803 REMARK 3 T TENSOR REMARK 3 T11: 0.1379 T22: 0.1240 REMARK 3 T33: 0.1248 T12: -0.0001 REMARK 3 T13: 0.0320 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.1995 L22: 0.3472 REMARK 3 L33: 0.3857 L12: 0.2875 REMARK 3 L13: -0.0905 L23: -0.2536 REMARK 3 S TENSOR REMARK 3 S11: -0.0318 S12: 0.0349 S13: 0.0075 REMARK 3 S21: -0.1600 S22: 0.0099 S23: -0.0980 REMARK 3 S31: -0.0122 S32: 0.0440 S33: -0.0251 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 334 THROUGH 404 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.2677 25.5639 39.1147 REMARK 3 T TENSOR REMARK 3 T11: 0.1102 T22: 0.1480 REMARK 3 T33: 0.1564 T12: -0.0305 REMARK 3 T13: 0.0181 T23: 0.0328 REMARK 3 L TENSOR REMARK 3 L11: 0.0968 L22: 0.1551 REMARK 3 L33: 0.1861 L12: 0.1350 REMARK 3 L13: -0.0020 L23: -0.0587 REMARK 3 S TENSOR REMARK 3 S11: 0.0067 S12: 0.0101 S13: -0.0447 REMARK 3 S21: -0.0125 S22: -0.0685 S23: -0.0823 REMARK 3 S31: -0.1540 S32: 0.1031 S33: -0.0880 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 405 THROUGH 489 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5464 18.9364 53.0182 REMARK 3 T TENSOR REMARK 3 T11: 0.1089 T22: 0.1198 REMARK 3 T33: 0.1315 T12: -0.0213 REMARK 3 T13: -0.0031 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 0.1173 L22: 0.2854 REMARK 3 L33: 0.3993 L12: 0.1881 REMARK 3 L13: -0.0935 L23: -0.2386 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: -0.0176 S13: 0.0093 REMARK 3 S21: 0.0648 S22: -0.0747 S23: -0.0437 REMARK 3 S31: -0.1086 S32: 0.0523 S33: -0.0285 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 6XM6 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_1000250142. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-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 : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 188761 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 43.847 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.330 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.15 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 6OJR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 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 42.74000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.09000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.37000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.74000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.09000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.37000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.74000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.09000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.37000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.74000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.09000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.37000 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 114.74000 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 727 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1231 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 GLY A 385 REMARK 465 SER A 386 REMARK 465 ALA A 387 REMARK 465 GLY A 388 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HD1 HIS A 445 HD1 HIS A 445 4556 1.13 REMARK 500 REMARK 500 REMARK: NULL 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 MET A 217 75.49 -100.50 REMARK 500 SER A 283 -61.58 -120.73 REMARK 500 PHE A 310 78.54 -119.68 REMARK 500 LEU A 475 -120.80 -106.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 356 0.08 SIDE CHAIN 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 A1383 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A1384 DISTANCE = 5.98 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 91.8 REMARK 620 3 HIS A 284 NE2 99.0 103.9 REMARK 620 4 HIS A 476 NE2 89.2 154.8 100.8 REMARK 620 5 HOH A 959 O 168.4 86.0 92.6 88.0 REMARK 620 N 1 2 3 4 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 DBREF 6XM6 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 HETNAM CO COBALT (II) ION FORMUL 2 CO CO 2+ FORMUL 3 HOH *784(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 ARG A 42 O THR A 66 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 GLN A 437 O LEU A 450 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 GLN A 437 O LEU A 450 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 ILE A 204 N GLU A 196 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 273 N ILE A 260 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 LYS A 398 N GLY A 369 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 2.12 LINK NE2 HIS A 218 CO CO A 501 1555 1555 2.01 LINK NE2 HIS A 284 CO CO A 501 1555 1555 2.05 LINK NE2 HIS A 476 CO CO A 501 1555 1555 2.02 LINK CO CO A 501 O HOH A 959 1555 1555 2.17 SITE 1 AC1 5 HIS A 167 HIS A 218 HIS A 284 HIS A 476 SITE 2 AC1 5 HOH A 959 CRYST1 85.480 112.180 114.740 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 0.011699 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008715 0.00000