HEADER OXIDOREDUCTASE 29-JUN-20 6XM7 TITLE CRYSTAL STRUCTURE OF DCA-S BOUND TO CO-LSD4 FROM SPHINGOBIUM SP. TITLE 2 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 6XM7 1 REMARK REVDAT 3 21-JUL-21 6XM7 1 JRNL REVDAT 2 26-MAY-21 6XM7 1 JRNL REVDAT 1 12-MAY-21 6XM7 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) : 43.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 184153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9207 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 43.8000 - 4.5039 1.00 5973 317 0.1574 0.1707 REMARK 3 2 4.5039 - 3.5754 1.00 5946 310 0.1153 0.1199 REMARK 3 3 3.5754 - 3.1236 1.00 5920 316 0.1282 0.1633 REMARK 3 4 3.1236 - 2.8380 1.00 5971 314 0.1283 0.1471 REMARK 3 5 2.8380 - 2.6347 1.00 5995 317 0.1229 0.1335 REMARK 3 6 2.6347 - 2.4793 1.00 5938 305 0.1156 0.1510 REMARK 3 7 2.4793 - 2.3552 1.00 5976 307 0.1190 0.1389 REMARK 3 8 2.3552 - 2.2527 1.00 5949 311 0.1194 0.1394 REMARK 3 9 2.2527 - 2.1659 1.00 5920 312 0.1088 0.1368 REMARK 3 10 2.1659 - 2.0912 1.00 5996 312 0.1110 0.1303 REMARK 3 11 2.0912 - 2.0258 1.00 5946 314 0.1125 0.1179 REMARK 3 12 2.0258 - 1.9679 1.00 5944 315 0.1195 0.1434 REMARK 3 13 1.9679 - 1.9161 1.00 5974 309 0.1170 0.1364 REMARK 3 14 1.9161 - 1.8694 0.99 5933 309 0.1210 0.1305 REMARK 3 15 1.8694 - 1.8269 1.00 5943 314 0.1244 0.1506 REMARK 3 16 1.8269 - 1.7880 1.00 5958 312 0.1312 0.1463 REMARK 3 17 1.7880 - 1.7522 1.00 5972 321 0.1211 0.1609 REMARK 3 18 1.7522 - 1.7191 1.00 5945 308 0.1244 0.1704 REMARK 3 19 1.7191 - 1.6884 1.00 5975 315 0.1271 0.1566 REMARK 3 20 1.6884 - 1.6598 1.00 5901 310 0.1311 0.1665 REMARK 3 21 1.6598 - 1.6330 1.00 6003 320 0.1402 0.1479 REMARK 3 22 1.6330 - 1.6079 1.00 5932 317 0.1489 0.1654 REMARK 3 23 1.6079 - 1.5843 1.00 5950 316 0.1666 0.1885 REMARK 3 24 1.5843 - 1.5620 1.00 5908 311 0.1986 0.2155 REMARK 3 25 1.5620 - 1.5408 0.99 5906 312 0.2314 0.2537 REMARK 3 26 1.5408 - 1.5208 0.98 5837 307 0.3071 0.3078 REMARK 3 27 1.5208 - 1.5018 0.92 5561 293 0.3133 0.3368 REMARK 3 28 1.5018 - 1.4837 0.88 5207 276 0.3305 0.3683 REMARK 3 29 1.4837 - 1.4665 0.83 4948 260 0.3583 0.3627 REMARK 3 30 1.4665 - 1.4500 0.77 4619 247 0.3987 0.3925 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.96 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 : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 358 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4331 14.0082 33.9915 REMARK 3 T TENSOR REMARK 3 T11: 0.1242 T22: 0.1352 REMARK 3 T33: 0.1326 T12: 0.0002 REMARK 3 T13: -0.0014 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.1534 L22: 0.5370 REMARK 3 L33: 0.4071 L12: 0.1098 REMARK 3 L13: -0.0330 L23: -0.2259 REMARK 3 S TENSOR REMARK 3 S11: -0.0098 S12: 0.0150 S13: 0.0028 REMARK 3 S21: -0.0871 S22: 0.0102 S23: 0.0037 REMARK 3 S31: 0.0281 S32: -0.0062 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 359 THROUGH 393 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.9914 20.6748 43.8367 REMARK 3 T TENSOR REMARK 3 T11: 0.1690 T22: 0.2046 REMARK 3 T33: 0.2245 T12: -0.0016 REMARK 3 T13: 0.0007 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 0.0411 L22: 0.0354 REMARK 3 L33: 0.0626 L12: 0.0268 REMARK 3 L13: 0.0346 L23: -0.0109 REMARK 3 S TENSOR REMARK 3 S11: 0.0622 S12: -0.0048 S13: -0.0772 REMARK 3 S21: -0.0334 S22: -0.0699 S23: -0.0960 REMARK 3 S31: -0.0073 S32: 0.1145 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 394 THROUGH 489 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4724 20.4312 52.1599 REMARK 3 T TENSOR REMARK 3 T11: 0.1430 T22: 0.1510 REMARK 3 T33: 0.1599 T12: -0.0152 REMARK 3 T13: -0.0043 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.0835 L22: 0.1208 REMARK 3 L33: 0.1702 L12: 0.0572 REMARK 3 L13: -0.0253 L23: -0.0696 REMARK 3 S TENSOR REMARK 3 S11: 0.0200 S12: -0.0246 S13: 0.0036 REMARK 3 S21: 0.0853 S22: -0.0467 S23: -0.0369 REMARK 3 S31: -0.0734 S32: 0.0438 S33: 0.0000 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 6XM7 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_1000250143. 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 : 184209 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 43.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.229 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6800 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 (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.43 REMARK 200 R MERGE FOR SHELL (I) : 0.50300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.940 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 (%): 50.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 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 42.66000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.01000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.33500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.66000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.01000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.33500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.66000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.01000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.33500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.66000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.01000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.33500 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 114.67000 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 815 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1011 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1141 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 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 LYS A 383 CG CD CE NZ 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 46 115.58 -161.43 REMARK 500 LEU A 475 -114.45 -108.76 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 A1275 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1276 DISTANCE = 6.16 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 510 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 167 NE2 REMARK 620 2 HIS A 218 NE2 95.5 REMARK 620 3 HIS A 284 NE2 100.3 107.2 REMARK 620 4 HIS A 476 NE2 91.4 149.5 100.6 REMARK 620 5 HOH A 885 O 165.8 83.1 93.5 83.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 514 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 314 NE2 REMARK 620 2 DMS A 507 O 99.4 REMARK 620 3 HOH A 625 O 105.8 80.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 511 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 373 OE1 REMARK 620 2 GLU A 373 OE2 64.1 REMARK 620 3 HIS A 407 ND1 74.0 93.0 REMARK 620 4 HOH A 634 O 136.1 75.3 93.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 512 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 448 OD1 REMARK 620 2 HIS A 466 ND1 83.9 REMARK 620 3 HOH A 682 O 82.7 166.5 REMARK 620 4 HOH A 862 O 106.4 123.5 62.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 515 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 783 O REMARK 620 2 HOH A 928 O 104.6 REMARK 620 3 HOH A 980 O 100.1 86.5 REMARK 620 4 HOH A1113 O 149.4 84.7 109.6 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 V5M A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS 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 DMS A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 515 DBREF 6XM7 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 V5M A 501 42 HET DMS A 502 10 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 DMS A 508 10 HET DMS A 509 10 HET CO A 510 1 HET CO A 511 1 HET CO A 512 1 HET CO A 513 1 HET CO A 514 1 HET MG A 515 1 HETNAM V5M (2E)-3-{4-HYDROXY-3-[(E)-2-(4-HYDROXY-3-METHOXYPHENYL) HETNAM 2 V5M ETHENYL]-5-METHOXYPHENYL}PROP-2-ENOIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETNAM CO COBALT (II) ION HETNAM MG MAGNESIUM ION FORMUL 2 V5M C19 H18 O6 FORMUL 3 DMS 8(C2 H6 O S) FORMUL 11 CO 5(CO 2+) FORMUL 16 MG MG 2+ FORMUL 17 HOH *676(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 ALA A 323 5 4 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 ALA A 480 N ALA A 39 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 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 SER A 325 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 LEU A 372 N GLU A 353 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 510 1555 1555 2.05 LINK NE2 HIS A 218 CO CO A 510 1555 1555 1.98 LINK NE2 HIS A 284 CO CO A 510 1555 1555 2.01 LINK NE2 HIS A 314 CO CO A 514 1555 1555 2.27 LINK OE1 GLU A 373 CO CO A 511 1555 1555 1.98 LINK OE2 GLU A 373 CO CO A 511 1555 1555 2.07 LINK ND1 HIS A 407 CO CO A 511 1555 1555 2.34 LINK OD1 ASP A 448 CO CO A 512 1555 1555 1.98 LINK ND1 HIS A 466 CO CO A 512 1555 1555 2.16 LINK NE2 HIS A 476 CO CO A 510 1555 1555 2.02 LINK O DMS A 507 CO CO A 514 1555 1555 2.21 LINK CO CO A 510 O HOH A 885 1555 1555 2.26 LINK CO CO A 511 O HOH A 634 1555 1555 2.17 LINK CO CO A 512 O HOH A 682 1555 1555 2.03 LINK CO CO A 512 O HOH A 862 1555 1555 1.99 LINK CO CO A 513 O HOH A1152 1555 1555 2.10 LINK CO CO A 514 O HOH A 625 1555 1555 2.10 LINK MG MG A 515 O HOH A 783 1555 1555 1.95 LINK MG MG A 515 O HOH A 928 1555 1555 2.06 LINK MG MG A 515 O HOH A 980 1555 1555 1.82 LINK MG MG A 515 O HOH A1113 1555 1555 2.02 SITE 1 AC1 19 PHE A 59 TYR A 101 ASN A 120 THR A 121 SITE 2 AC1 19 LYS A 134 HIS A 218 SER A 283 HIS A 284 SITE 3 AC1 19 MET A 306 PHE A 307 GLU A 353 PHE A 354 SITE 4 AC1 19 SER A 386 ALA A 387 PHE A 390 MET A 392 SITE 5 AC1 19 PHE A 473 LEU A 475 HOH A 885 SITE 1 AC2 8 GLU A 35 LEU A 36 ASN A 37 PRO A 423 SITE 2 AC2 8 ARG A 424 TRP A 434 TRP A 479 ASN A 481 SITE 1 AC3 4 ASP A 55 ASP A 56 HOH A 626 HOH A 763 SITE 1 AC4 5 ARG A 360 ALA A 428 GLU A 430 HOH A 610 SITE 2 AC4 5 HOH A 648 SITE 1 AC5 4 GLY A 113 GLU A 114 GLN A 162 HOH A1048 SITE 1 AC6 5 GLU A 29 PRO A 461 VAL A 462 ALA A 463 SITE 2 AC6 5 THR A 464 SITE 1 AC7 5 VAL A 313 HIS A 314 CO A 514 HOH A 625 SITE 2 AC7 5 HOH A 954 SITE 1 AC8 5 THR A 141 GLY A 151 PHE A 152 GLU A 153 SITE 2 AC8 5 HOH A1254 SITE 1 AC9 3 GLY A 113 TYR A 115 HOH A 636 SITE 1 AD1 5 HIS A 167 HIS A 218 HIS A 284 HIS A 476 SITE 2 AD1 5 HOH A 885 SITE 1 AD2 4 GLU A 373 CYS A 394 HIS A 407 HOH A 634 SITE 1 AD3 5 ASP A 448 HIS A 466 HOH A 682 HOH A 862 SITE 2 AD3 5 HOH A 957 SITE 1 AD4 2 ASN A 481 HOH A1152 SITE 1 AD5 3 HIS A 314 DMS A 507 HOH A 625 SITE 1 AD6 4 HOH A 783 HOH A 928 HOH A 980 HOH A1113 CRYST1 85.320 112.020 114.670 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 0.011721 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008927 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008721 0.00000