HEADER OXIDOREDUCTASE 29-JUN-20 6XMA TITLE CRYSTAL STRUCTURE OF IRON-BOUND LSD4 FROM SPHINGOBIUM 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 6XMA 1 REMARK REVDAT 3 21-JUL-21 6XMA 1 JRNL REVDAT 2 26-MAY-21 6XMA 1 JRNL REVDAT 1 12-MAY-21 6XMA 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) : 29.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 188515 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9418 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 29.7880 - 4.4992 0.99 6001 344 0.1445 0.1719 REMARK 3 2 4.4992 - 3.5731 0.99 6004 334 0.1197 0.1178 REMARK 3 3 3.5731 - 3.1220 0.99 5997 296 0.1339 0.1586 REMARK 3 4 3.1220 - 2.8368 0.97 5906 308 0.1434 0.1539 REMARK 3 5 2.8368 - 2.6336 0.97 5851 339 0.1403 0.1592 REMARK 3 6 2.6336 - 2.4784 0.97 5910 276 0.1403 0.1601 REMARK 3 7 2.4784 - 2.3543 0.97 5926 315 0.1350 0.1576 REMARK 3 8 2.3543 - 2.2519 0.98 5986 268 0.1382 0.1623 REMARK 3 9 2.2519 - 2.1652 0.99 5964 343 0.1344 0.1749 REMARK 3 10 2.1652 - 2.0905 0.99 6008 342 0.1430 0.1522 REMARK 3 11 2.0905 - 2.0252 0.99 5982 314 0.1393 0.1473 REMARK 3 12 2.0252 - 1.9673 0.99 6001 341 0.1528 0.1594 REMARK 3 13 1.9673 - 1.9155 0.99 6053 307 0.1521 0.1966 REMARK 3 14 1.9155 - 1.8688 0.99 6004 301 0.1630 0.2041 REMARK 3 15 1.8688 - 1.8263 0.99 5982 330 0.1786 0.1977 REMARK 3 16 1.8263 - 1.7875 0.99 6046 321 0.1798 0.2314 REMARK 3 17 1.7875 - 1.7517 1.00 6085 289 0.1660 0.1872 REMARK 3 18 1.7517 - 1.7186 1.00 6062 321 0.1751 0.1947 REMARK 3 19 1.7186 - 1.6880 1.00 6081 313 0.1607 0.2130 REMARK 3 20 1.6880 - 1.6593 1.00 6058 318 0.1605 0.1857 REMARK 3 21 1.6593 - 1.6326 1.00 6087 306 0.1633 0.2144 REMARK 3 22 1.6326 - 1.6075 1.00 6114 314 0.1650 0.1796 REMARK 3 23 1.6075 - 1.5838 1.00 6013 350 0.1659 0.2029 REMARK 3 24 1.5838 - 1.5615 1.00 6167 297 0.1714 0.2048 REMARK 3 25 1.5615 - 1.5404 1.00 6053 305 0.1657 0.1814 REMARK 3 26 1.5404 - 1.5204 1.00 6045 317 0.1742 0.2240 REMARK 3 27 1.5204 - 1.5014 1.00 6104 320 0.1806 0.2265 REMARK 3 28 1.5014 - 1.4833 1.00 6087 322 0.1978 0.2284 REMARK 3 29 1.4833 - 1.4661 0.94 5747 298 0.2385 0.2661 REMARK 3 30 1.4661 - 1.4500 0.80 4773 269 0.2732 0.2720 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.93 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 405 THROUGH 489 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.6803 18.9800 53.1985 REMARK 3 T TENSOR REMARK 3 T11: 0.0953 T22: 0.0955 REMARK 3 T33: 0.0949 T12: -0.0293 REMARK 3 T13: -0.0027 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.1183 L22: 0.3575 REMARK 3 L33: 0.4293 L12: 0.2287 REMARK 3 L13: -0.1497 L23: -0.3049 REMARK 3 S TENSOR REMARK 3 S11: 0.0434 S12: -0.0299 S13: 0.0107 REMARK 3 S21: 0.0794 S22: -0.0805 S23: -0.0458 REMARK 3 S31: -0.1176 S32: 0.0874 S33: -0.0476 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 237 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9874 9.5371 38.4772 REMARK 3 T TENSOR REMARK 3 T11: 0.0594 T22: 0.0728 REMARK 3 T33: 0.0704 T12: -0.0023 REMARK 3 T13: 0.0014 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.0904 L22: 0.3834 REMARK 3 L33: 0.3604 L12: 0.1358 REMARK 3 L13: -0.0336 L23: -0.1690 REMARK 3 S TENSOR REMARK 3 S11: -0.0032 S12: 0.0151 S13: 0.0146 REMARK 3 S21: -0.0453 S22: 0.0162 S23: 0.0175 REMARK 3 S31: 0.0190 S32: -0.0029 S33: 0.0241 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 238 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6153 17.9048 19.5098 REMARK 3 T TENSOR REMARK 3 T11: 0.1505 T22: 0.1194 REMARK 3 T33: 0.1139 T12: -0.0100 REMARK 3 T13: 0.0223 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 0.1423 L22: 0.1450 REMARK 3 L33: 0.2159 L12: 0.1725 REMARK 3 L13: -0.0450 L23: -0.1290 REMARK 3 S TENSOR REMARK 3 S11: -0.0515 S12: 0.1077 S13: 0.0066 REMARK 3 S21: -0.2019 S22: 0.0397 S23: -0.0141 REMARK 3 S31: 0.0472 S32: -0.0073 S33: -0.0075 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 358 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.4315 23.5761 29.3565 REMARK 3 T TENSOR REMARK 3 T11: 0.0994 T22: 0.1152 REMARK 3 T33: 0.1159 T12: -0.0112 REMARK 3 T13: 0.0248 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 0.1708 L22: 0.2354 REMARK 3 L33: 0.3763 L12: 0.3149 REMARK 3 L13: -0.0732 L23: -0.2056 REMARK 3 S TENSOR REMARK 3 S11: -0.0008 S12: 0.0065 S13: -0.0450 REMARK 3 S21: -0.0378 S22: -0.0232 S23: -0.0809 REMARK 3 S31: -0.0685 S32: 0.1022 S33: -0.0013 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 359 THROUGH 404 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.6601 25.4575 44.4017 REMARK 3 T TENSOR REMARK 3 T11: 0.0865 T22: 0.1182 REMARK 3 T33: 0.1319 T12: -0.0535 REMARK 3 T13: 0.0095 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 0.0509 L22: 0.0762 REMARK 3 L33: 0.2028 L12: 0.0850 REMARK 3 L13: -0.0637 L23: -0.0431 REMARK 3 S TENSOR REMARK 3 S11: 0.0014 S12: -0.0472 S13: -0.0574 REMARK 3 S21: 0.0143 S22: -0.0686 S23: -0.0809 REMARK 3 S31: -0.1927 S32: 0.0947 S33: -0.0338 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 6XMA 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_1000250146. 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 : 190316 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 16.10 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 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) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.55800 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 (%): 51.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M MAGNESIUM ACETATE AND 28% REMARK 280 PEG3350, PH 8, VAPOR DIFFUSION, SITTING 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 43.01500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.26350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.69200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.01500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.26350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.69200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.01500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.26350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.69200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.01500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.26350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.69200 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 115.38400 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 705 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1337 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1446 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES 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 SER A 17 -68.25 -108.15 REMARK 500 MET A 217 72.68 -102.22 REMARK 500 LEU A 475 -119.56 -104.89 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 A1467 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A1468 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A1469 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A1470 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A1471 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A1472 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A1473 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A1474 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A1475 DISTANCE = 7.36 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 FE A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 167 NE2 REMARK 620 2 HIS A 218 NE2 89.5 REMARK 620 3 HIS A 284 NE2 97.7 101.2 REMARK 620 4 HIS A 476 NE2 89.5 157.3 101.4 REMARK 620 5 HOH A1100 O 173.9 90.3 88.3 88.4 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 SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 502 DBREF 6XMA 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 SO4 A 501 5 HET FE A 502 1 HETNAM SO4 SULFATE ION HETNAM FE FE (III) ION FORMUL 2 SO4 O4 S 2- FORMUL 3 FE FE 3+ FORMUL 4 HOH *875(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 SER A 237 LYS A 243 1 7 HELIX 7 AA7 LYS A 268 ILE A 272 5 5 HELIX 8 AA8 ASP A 358 THR A 362 5 5 HELIX 9 AA9 ALA A 443 HIS A 445 5 3 HELIX 10 AB1 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 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 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 FE FE A 502 1555 1555 2.25 LINK NE2 HIS A 218 FE FE A 502 1555 1555 2.00 LINK NE2 HIS A 284 FE FE A 502 1555 1555 2.08 LINK NE2 HIS A 476 FE FE A 502 1555 1555 2.06 LINK FE FE A 502 O HOH A1100 1555 1555 2.26 SITE 1 AC1 11 PHE A 59 TYR A 101 THR A 121 LYS A 134 SITE 2 AC1 11 GLU A 135 HIS A 218 HOH A 607 HOH A 611 SITE 3 AC1 11 HOH A 616 HOH A 620 HOH A 682 SITE 1 AC2 5 HIS A 167 HIS A 218 HIS A 284 HIS A 476 SITE 2 AC2 5 HOH A1100 CRYST1 86.030 112.527 115.384 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 0.011624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008667 0.00000