HEADER OXIDOREDUCTASE 29-JUN-20 6XM9 TITLE CRYSTAL STRUCTURE OF VANILLIN 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 6XM9 1 REMARK REVDAT 3 21-JUL-21 6XM9 1 JRNL REVDAT 2 26-MAY-21 6XM9 1 JRNL REVDAT 1 12-MAY-21 6XM9 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 127346 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6489 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 29.7120 - 5.1203 0.99 4043 203 0.1852 0.2039 REMARK 3 2 5.1203 - 4.0674 0.98 3934 265 0.1235 0.1506 REMARK 3 3 4.0674 - 3.5542 0.99 4027 196 0.1269 0.1436 REMARK 3 4 3.5542 - 3.2297 0.99 4000 217 0.1392 0.1468 REMARK 3 5 3.2297 - 2.9984 0.98 3996 191 0.1461 0.1596 REMARK 3 6 2.9984 - 2.8218 0.98 3998 200 0.1513 0.1779 REMARK 3 7 2.8218 - 2.6806 0.98 3963 219 0.1549 0.1875 REMARK 3 8 2.6806 - 2.5640 0.99 4034 231 0.1486 0.2033 REMARK 3 9 2.5640 - 2.4653 0.99 3987 204 0.1504 0.2023 REMARK 3 10 2.4653 - 2.3803 0.99 4097 196 0.1461 0.1567 REMARK 3 11 2.3803 - 2.3059 1.00 4025 222 0.1448 0.1936 REMARK 3 12 2.3059 - 2.2400 1.00 4040 227 0.1479 0.1694 REMARK 3 13 2.2400 - 2.1810 1.00 4077 193 0.1483 0.1962 REMARK 3 14 2.1810 - 2.1278 1.00 4030 193 0.1491 0.2253 REMARK 3 15 2.1278 - 2.0795 1.00 4049 232 0.1573 0.2031 REMARK 3 16 2.0795 - 2.0352 1.00 4068 219 0.1579 0.1748 REMARK 3 17 2.0352 - 1.9945 1.00 4098 222 0.1698 0.2109 REMARK 3 18 1.9945 - 1.9569 1.00 4026 218 0.1715 0.1953 REMARK 3 19 1.9569 - 1.9220 1.00 4050 225 0.1674 0.2006 REMARK 3 20 1.9220 - 1.8894 1.00 3975 217 0.1810 0.2171 REMARK 3 21 1.8894 - 1.8589 1.00 4070 236 0.1809 0.1981 REMARK 3 22 1.8589 - 1.8303 1.00 4082 220 0.1894 0.2241 REMARK 3 23 1.8303 - 1.8034 1.00 4089 216 0.1873 0.2270 REMARK 3 24 1.8034 - 1.7780 1.00 3998 213 0.2030 0.2233 REMARK 3 25 1.7780 - 1.7540 1.00 4078 198 0.1990 0.2439 REMARK 3 26 1.7540 - 1.7312 1.00 4103 219 0.2070 0.2038 REMARK 3 27 1.7312 - 1.7096 1.00 3991 243 0.2137 0.2336 REMARK 3 28 1.7096 - 1.6890 1.00 4063 224 0.2250 0.2910 REMARK 3 29 1.6890 - 1.6693 0.99 3998 240 0.2410 0.2507 REMARK 3 30 1.6693 - 1.6510 0.95 3868 190 0.2543 0.2736 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.26 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 : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 359 THROUGH 404 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.4150 25.9705 44.7170 REMARK 3 T TENSOR REMARK 3 T11: 0.0878 T22: 0.1213 REMARK 3 T33: 0.1402 T12: -0.0314 REMARK 3 T13: 0.0011 T23: 0.0295 REMARK 3 L TENSOR REMARK 3 L11: 0.0640 L22: 0.1076 REMARK 3 L33: 0.2485 L12: 0.0696 REMARK 3 L13: -0.1084 L23: -0.1049 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: 0.0093 S13: -0.0206 REMARK 3 S21: 0.0152 S22: -0.0730 S23: -0.1041 REMARK 3 S31: -0.1156 S32: 0.0836 S33: -0.0153 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 405 THROUGH 489 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.4187 19.0704 53.4224 REMARK 3 T TENSOR REMARK 3 T11: 0.0811 T22: 0.0916 REMARK 3 T33: 0.0919 T12: -0.0165 REMARK 3 T13: -0.0053 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.1014 L22: 0.3262 REMARK 3 L33: 0.3930 L12: 0.1886 REMARK 3 L13: -0.1042 L23: -0.3412 REMARK 3 S TENSOR REMARK 3 S11: 0.0438 S12: -0.0203 S13: -0.0041 REMARK 3 S21: 0.0936 S22: -0.0661 S23: -0.0246 REMARK 3 S31: -0.0733 S32: 0.0519 S33: -0.0055 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 237 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7036 9.8173 38.4948 REMARK 3 T TENSOR REMARK 3 T11: 0.0641 T22: 0.0814 REMARK 3 T33: 0.0834 T12: -0.0070 REMARK 3 T13: -0.0107 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.1182 L22: 0.5612 REMARK 3 L33: 0.4632 L12: 0.0246 REMARK 3 L13: 0.0730 L23: -0.2857 REMARK 3 S TENSOR REMARK 3 S11: 0.0051 S12: 0.0081 S13: 0.0019 REMARK 3 S21: -0.0773 S22: 0.0284 S23: 0.0714 REMARK 3 S31: 0.0536 S32: -0.0235 S33: 0.0347 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 238 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4829 18.1480 19.6378 REMARK 3 T TENSOR REMARK 3 T11: 0.1677 T22: 0.1271 REMARK 3 T33: 0.1041 T12: 0.0021 REMARK 3 T13: 0.0086 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 0.1589 L22: 0.1906 REMARK 3 L33: 0.2778 L12: 0.1842 REMARK 3 L13: 0.0096 L23: -0.1030 REMARK 3 S TENSOR REMARK 3 S11: -0.0117 S12: 0.1181 S13: 0.0335 REMARK 3 S21: -0.2801 S22: 0.0069 S23: 0.0115 REMARK 3 S31: 0.0896 S32: -0.0225 S33: -0.0019 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 358 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.3464 23.6013 29.6170 REMARK 3 T TENSOR REMARK 3 T11: 0.0913 T22: 0.1184 REMARK 3 T33: 0.1128 T12: -0.0030 REMARK 3 T13: 0.0182 T23: 0.0240 REMARK 3 L TENSOR REMARK 3 L11: 0.1050 L22: 0.2629 REMARK 3 L33: 0.4063 L12: 0.2185 REMARK 3 L13: -0.0794 L23: -0.1263 REMARK 3 S TENSOR REMARK 3 S11: -0.0024 S12: -0.0071 S13: -0.0393 REMARK 3 S21: -0.0533 S22: -0.0353 S23: -0.0574 REMARK 3 S31: -0.0579 S32: 0.0931 S33: -0.0144 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 6XM9 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_1000250145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127993 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.58400 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 6OJR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.88 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 42.58000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.07850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.65550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.58000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.07850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.65550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.58000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.07850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.65550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.58000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.07850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.65550 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 115.31100 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 697 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 970 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1144 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 LEU A 382 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 465 GLY A 388 REMARK 465 GLY A 389 REMARK 465 PHE A 390 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 46 109.76 -161.63 REMARK 500 MET A 217 75.16 -101.77 REMARK 500 LEU A 475 -116.37 -103.93 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 A1301 DISTANCE = 6.63 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 511 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 167 NE2 REMARK 620 2 HIS A 218 NE2 92.1 REMARK 620 3 HIS A 284 NE2 100.5 102.3 REMARK 620 4 HIS A 476 NE2 88.3 157.8 99.5 REMARK 620 5 HOH A 612 O 156.4 87.0 102.8 83.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 513 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 646 O REMARK 620 2 HOH A 672 O 82.2 REMARK 620 3 HOH A 691 O 92.6 133.4 REMARK 620 4 HOH A 713 O 87.9 67.3 66.3 REMARK 620 5 HOH A1039 O 91.8 133.9 92.4 158.6 REMARK 620 6 HOH A1183 O 160.5 85.5 84.9 73.4 107.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 514 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 603 O REMARK 620 2 HOH A 709 O 110.4 REMARK 620 3 HOH A1046 O 165.1 81.1 REMARK 620 4 HOH A1130 O 108.2 94.3 79.3 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 V55 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 ACT 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 DMS 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 MG A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 514 DBREF 6XM9 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 V55 A 501 11 HET DMS A 502 10 HET DMS A 503 10 HET DMS A 504 10 HET DMS A 505 10 HET ACT A 506 7 HET DMS A 507 10 HET DMS A 508 10 HET DMS A 509 10 HET DMS A 510 10 HET CO A 511 1 HET CO A 512 1 HET MG A 513 1 HET MG A 514 1 HETNAM V55 4-HYDROXY-3-METHOXYBENZALDEHYDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM ACT ACETATE ION HETNAM CO COBALT (II) ION HETNAM MG MAGNESIUM ION HETSYN V55 P-VANILLIN FORMUL 2 V55 C8 H8 O3 FORMUL 3 DMS 8(C2 H6 O S) FORMUL 7 ACT C2 H3 O2 1- FORMUL 12 CO 2(CO 2+) FORMUL 14 MG 2(MG 2+) FORMUL 16 HOH *701(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 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 LEU A 467 -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 LEU A 467 -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 GLY A 151 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 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 511 1555 1555 2.12 LINK NE2 HIS A 218 CO CO A 511 1555 1555 2.08 LINK NE2 HIS A 284 CO CO A 511 1555 1555 2.01 LINK NE2 HIS A 476 CO CO A 511 1555 1555 2.03 LINK CO CO A 511 O HOH A 612 1555 1555 2.16 LINK MG MG A 513 O HOH A 646 1555 1555 2.19 LINK MG MG A 513 O HOH A 672 1555 1555 1.98 LINK MG MG A 513 O HOH A 691 1555 1555 2.05 LINK MG MG A 513 O HOH A 713 1555 1555 2.97 LINK MG MG A 513 O HOH A1039 1555 1555 1.90 LINK MG MG A 513 O HOH A1183 1555 2555 2.10 LINK MG MG A 514 O HOH A 603 1555 1555 1.96 LINK MG MG A 514 O HOH A 709 1555 1555 2.50 LINK MG MG A 514 O HOH A1046 1555 1555 2.37 LINK MG MG A 514 O HOH A1130 1555 1555 2.10 SITE 1 AC1 10 PHE A 59 TYR A 101 ASN A 120 THR A 121 SITE 2 AC1 10 LYS A 134 MET A 216 HIS A 218 LEU A 475 SITE 3 AC1 10 HOH A 612 HOH A 817 SITE 1 AC2 7 LEU A 36 PRO A 423 ARG A 424 TRP A 434 SITE 2 AC2 7 TRP A 479 ASN A 481 HOH A 757 SITE 1 AC3 5 ARG A 360 LYS A 426 ALA A 428 GLU A 430 SITE 2 AC3 5 HOH A 676 SITE 1 AC4 4 ASP A 55 ASP A 56 HOH A 635 HOH A 687 SITE 1 AC5 3 GLU A 114 GLN A 162 HOH A 663 SITE 1 AC6 7 PHE A 155 LYS A 158 GLU A 202 LEU A 203 SITE 2 AC6 7 HOH A 646 HOH A 672 HOH A 922 SITE 1 AC7 5 ALA A 92 THR A 141 GLY A 151 PHE A 152 SITE 2 AC7 5 GLU A 153 SITE 1 AC8 4 PRO A 461 VAL A 462 ALA A 463 THR A 464 SITE 1 AC9 4 HIS A 400 GLN A 401 THR A 402 GLY A 403 SITE 1 AD1 5 ARG A 346 LEU A 347 THR A 348 GLU A 349 SITE 2 AD1 5 HOH A1107 SITE 1 AD2 5 HIS A 167 HIS A 218 HIS A 284 HIS A 476 SITE 2 AD2 5 HOH A 612 SITE 1 AD3 2 LYS A 158 ARG A 346 SITE 1 AD4 6 HOH A 646 HOH A 672 HOH A 691 HOH A 713 SITE 2 AD4 6 HOH A1039 HOH A1183 SITE 1 AD5 4 HOH A 603 HOH A 709 HOH A1046 HOH A1130 CRYST1 85.160 112.157 115.311 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 0.011743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008916 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008672 0.00000