HEADER BIOSYNTHETIC PROTEIN 28-NOV-17 5YVZ TITLE CRYSTAL STRUCTURE OF THE KDO HYDROXYLASE KDOO, A NON-HEME FE(II) TITLE 2 ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE IN COMPLEX WITH TITLE 3 ALPHAKETOGLUTARATE AND FE(III) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN KDOO; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3-DEOXY-D-MANNO-OCTULOSONIC ACID HYDORXYLASE,KDO COMPND 5 HYDROXYLASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLACIDIPHILUM INFERNORUM (ISOLATE V4); SOURCE 3 ORGANISM_COMMON: ISOLATE V4; SOURCE 4 ORGANISM_TAXID: 481448; SOURCE 5 GENE: MINF_1012; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FE(II)/O2/ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE, KDO2-LIPID A KEYWDS 2 DIOXYGENASE, DEOXYSUGAR DIOXYGENASE, LPS BIOSYNTHESIS, BIOSYNTHETIC KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.S.CHUNG,C.W.PEMBLE,S.H.JOO,C.R.RAETZ REVDAT 3 22-NOV-23 5YVZ 1 REMARK LINK REVDAT 2 24-OCT-18 5YVZ 1 JRNL REVDAT 1 05-SEP-18 5YVZ 0 JRNL AUTH S.H.JOO,C.W.PEMBLE,E.G.YANG,C.R.H.RAETZ,H.S.CHUNG JRNL TITL BIOCHEMICAL AND STRUCTURAL INSIGHTS INTO AN FE(II)/ JRNL TITL 2 ALPHA-KETOGLUTARATE/O2-DEPENDENT DIOXYGENASE, KDO JRNL TITL 3 3-HYDROXYLASE (KDOO). JRNL REF J. MOL. BIOL. V. 430 4036 2018 JRNL REFN ESSN 1089-8638 JRNL PMID 30092253 JRNL DOI 10.1016/J.JMB.2018.07.029 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 41632 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2082 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 34.5549 - 3.9435 0.99 2862 152 0.1658 0.1818 REMARK 3 2 3.9435 - 3.1307 1.00 2761 145 0.1449 0.1584 REMARK 3 3 3.1307 - 2.7352 1.00 2735 144 0.1651 0.1929 REMARK 3 4 2.7352 - 2.4852 1.00 2703 142 0.1619 0.1737 REMARK 3 5 2.4852 - 2.3071 1.00 2677 141 0.1600 0.2137 REMARK 3 6 2.3071 - 2.1711 1.00 2677 141 0.1543 0.1681 REMARK 3 7 2.1711 - 2.0624 1.00 2672 141 0.1526 0.1928 REMARK 3 8 2.0624 - 1.9726 1.00 2636 138 0.1524 0.1657 REMARK 3 9 1.9726 - 1.8967 0.99 2667 138 0.1544 0.1758 REMARK 3 10 1.8967 - 1.8312 0.99 2627 140 0.1569 0.2147 REMARK 3 11 1.8312 - 1.7740 0.99 2645 138 0.1565 0.1685 REMARK 3 12 1.7740 - 1.7233 0.98 2598 139 0.1652 0.1938 REMARK 3 13 1.7233 - 1.6779 0.97 2558 133 0.1726 0.2273 REMARK 3 14 1.6779 - 1.6370 0.94 2486 133 0.1932 0.1851 REMARK 3 15 1.6370 - 1.5997 0.85 2246 117 0.2031 0.2660 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.46 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 : 0.005 2516 REMARK 3 ANGLE : 0.790 3387 REMARK 3 CHIRALITY : 0.054 361 REMARK 3 PLANARITY : 0.005 431 REMARK 3 DIHEDRAL : 16.809 1525 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 11 THROUGH 127 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.1335 3.3933 -6.0800 REMARK 3 T TENSOR REMARK 3 T11: 0.1155 T22: 0.1184 REMARK 3 T33: 0.1322 T12: -0.0029 REMARK 3 T13: 0.0220 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 1.8303 L22: 2.6032 REMARK 3 L33: 2.7250 L12: 0.5536 REMARK 3 L13: 0.7744 L23: 0.4870 REMARK 3 S TENSOR REMARK 3 S11: -0.0054 S12: -0.1436 S13: 0.0777 REMARK 3 S21: 0.2024 S22: -0.0492 S23: -0.1191 REMARK 3 S31: -0.1685 S32: 0.0304 S33: 0.0305 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 128 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9546 -2.2915 -17.6360 REMARK 3 T TENSOR REMARK 3 T11: 0.2978 T22: 0.3974 REMARK 3 T33: 0.5698 T12: -0.0140 REMARK 3 T13: -0.0045 T23: -0.0508 REMARK 3 L TENSOR REMARK 3 L11: 0.3533 L22: 8.0811 REMARK 3 L33: 6.7600 L12: 0.7339 REMARK 3 L13: 0.4625 L23: 7.3148 REMARK 3 S TENSOR REMARK 3 S11: 0.1277 S12: -0.1564 S13: -0.2982 REMARK 3 S21: 0.1940 S22: 0.8040 S23: -1.7863 REMARK 3 S31: 0.3558 S32: 0.9920 S33: -0.7813 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 146 THROUGH 307 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9383 -11.5084 -17.0725 REMARK 3 T TENSOR REMARK 3 T11: 0.1027 T22: 0.1237 REMARK 3 T33: 0.1027 T12: 0.0028 REMARK 3 T13: -0.0009 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.4922 L22: 1.8083 REMARK 3 L33: 0.9180 L12: -0.0782 REMARK 3 L13: 0.0109 L23: 0.1667 REMARK 3 S TENSOR REMARK 3 S11: 0.0503 S12: 0.0416 S13: -0.0329 REMARK 3 S21: 0.0121 S22: -0.0453 S23: -0.0692 REMARK 3 S31: 0.1276 S32: 0.0509 S33: -0.0130 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 5YVZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41701 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.46800 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: PHENIX REMARK 200 STARTING MODEL: 5Y7S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE (PH=4.5), 200MM REMARK 280 LITHIUM SULFATE, 50 % V/V PEG 400, PH 4.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 22.85500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.13200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.60200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.13200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.85500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.60200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 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 PHE A 2 REMARK 465 PRO A 3 REMARK 465 MET A 4 REMARK 465 ASP A 5 REMARK 465 THR A 6 REMARK 465 LYS A 7 REMARK 465 THR A 8 REMARK 465 ASN A 9 REMARK 465 GLU A 10 REMARK 465 GLY A 67 REMARK 465 ALA A 68 REMARK 465 LYS A 69 REMARK 465 ALA A 308 REMARK 465 ALA A 309 REMARK 465 ALA A 310 REMARK 465 LEU A 311 REMARK 465 GLU A 312 REMARK 465 HIS A 313 REMARK 465 HIS A 314 REMARK 465 HIS A 315 REMARK 465 HIS A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 55 CD REMARK 480 GLU A 130 CD REMARK 480 GLN A 183 CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 542 O HOH A 568 2.14 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 ALA A 122 -144.98 -126.67 REMARK 500 PHE A 267 93.20 84.55 REMARK 500 GLU A 303 136.00 -39.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 404 REMARK 610 PG4 A 405 REMARK 610 PG4 A 406 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 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 146 NE2 REMARK 620 2 ASP A 148 OD1 92.9 REMARK 620 3 HIS A 260 NE2 88.5 96.6 REMARK 620 4 AKG A 402 O1 166.5 99.2 95.9 REMARK 620 5 AKG A 402 O5 90.4 171.3 91.4 76.8 REMARK 620 6 HOH A 582 O 80.1 82.7 168.6 95.5 90.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 410 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5Y7S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE KDO HYDROXYLASE KDOO, A NON-HEME FE(II) REMARK 900 ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE REMARK 900 RELATED ID: 5YKA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE KDO HYDROXYLASE KDOO, A NON-HEME FE(II) REMARK 900 ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE IN COMPLEX WITH CO(II) REMARK 900 RELATED ID: 5Y9X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE KDO HYDROXYLASE KDOO, A NON-HEME FE(II) REMARK 900 ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE IN COMPLEX WITH REMARK 900 ALPHAKETOGLUTARATE AND CO(II) REMARK 900 RELATED ID: 5Y9Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE KDO HYDROXYLASE KDOO, A NON-HEME FE(II) REMARK 900 ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE IN COMPLEX WITH SUCCINATE REMARK 900 AND CO(II) DBREF 5YVZ A 1 305 UNP B3DUR4 B3DUR4_METI4 1 305 SEQADV 5YVZ LYS A 306 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ LEU A 307 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ ALA A 308 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ ALA A 309 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ ALA A 310 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ LEU A 311 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ GLU A 312 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ HIS A 313 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ HIS A 314 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ HIS A 315 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ HIS A 316 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ HIS A 317 UNP B3DUR4 EXPRESSION TAG SEQADV 5YVZ HIS A 318 UNP B3DUR4 EXPRESSION TAG SEQRES 1 A 318 MET PHE PRO MET ASP THR LYS THR ASN GLU GLN PRO ILE SEQRES 2 A 318 ILE GLN PHE ASP ALA GLU SER TRP GLU ALA GLU PHE THR SEQRES 3 A 318 GLN GLU ILE GLN ASP LYS ALA ILE GLU GLY LEU GLU SER SEQRES 4 A 318 GLY SER VAL LEU PHE PHE PRO LYS LEU ASN PHE PRO LEU SEQRES 5 A 318 LEU THR GLU GLU LEU LYS PHE LEU ASP PRO THR TRP VAL SEQRES 6 A 318 SER GLY ALA LYS ASN ILE SER TYR ASP PRO ARG SER ALA SEQRES 7 A 318 THR LEU LYS GLY VAL GLU GLY LYS SER GLU ASP LEU ARG SEQRES 8 A 318 LEU LEU SER GLY LEU LEU LYS ARG TYR ALA GLU LYS THR SEQRES 9 A 318 ALA ALA PHE LEU HIS LEU LEU PHE PRO PHE TYR GLY SER SEQRES 10 A 318 SER LEU LYS ILE ALA ARG THR SER PHE ARG PRO VAL GLU SEQRES 11 A 318 ILE SER GLY ARG ALA THR SER ALA ARG LYS ASP ASP THR SEQRES 12 A 318 ARG LEU HIS VAL ASP ALA PHE PRO SER SER PRO THR GLY SEQRES 13 A 318 GLY GLU ARG ILE LEU ARG VAL PHE SER ASN ILE ASN PRO SEQRES 14 A 318 GLN GLY LYS PRO ARG SER TRP ARG ILE GLY GLU PRO PHE SEQRES 15 A 318 GLN ASN TYR LEU ASN HIS LEU LEU PRO GLN LEU SER PRO SEQRES 16 A 318 PRO ALA PRO GLY LYS ARG PHE LEU LEU TYR LEU PHE GLY SEQRES 17 A 318 ILE THR LYS GLY TYR ARG SER LEU TYR ASP HIS TYR MET SEQRES 18 A 318 LEU GLU LEU HIS ASP LYS GLY LYS LEU ASP LEU GLU TYR SEQRES 19 A 318 GLN LYS ASN SER PRO GLN VAL ALA PHE ASP PHE PRO ALA SEQRES 20 A 318 GLY SER THR TRP ILE VAL PHE THR ASP GLN VAL LEU HIS SEQRES 21 A 318 ALA VAL ASP LYS GLY GLN PHE LEU LEU GLU GLN THR PHE SEQRES 22 A 318 HIS LEU LYS VAL ASN ALA LEU LYS HIS PRO GLU LYS SER SEQRES 23 A 318 PRO LEU LYS LEU LEU GLU THR ALA LEU ASN LYS LYS LEU SEQRES 24 A 318 VAL SER SER GLU SER PHE LYS LEU ALA ALA ALA LEU GLU SEQRES 25 A 318 HIS HIS HIS HIS HIS HIS HET FE A 401 1 HET AKG A 402 10 HET GOL A 403 6 HET PG4 A 404 10 HET PG4 A 405 10 HET PG4 A 406 10 HET PG4 A 407 13 HET ACT A 408 4 HET ACT A 409 4 HET SO4 A 410 5 HETNAM FE FE (III) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM GOL GLYCEROL HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FE FE 3+ FORMUL 3 AKG C5 H6 O5 FORMUL 4 GOL C3 H8 O3 FORMUL 5 PG4 4(C8 H18 O5) FORMUL 9 ACT 2(C2 H3 O2 1-) FORMUL 11 SO4 O4 S 2- FORMUL 12 HOH *166(H2 O) HELIX 1 AA1 THR A 26 SER A 39 1 14 HELIX 2 AA2 LEU A 53 LEU A 60 5 8 HELIX 3 AA3 ASP A 61 VAL A 65 5 5 HELIX 4 AA4 LYS A 86 PHE A 112 1 27 HELIX 5 AA5 PRO A 113 LEU A 119 5 7 HELIX 6 AA6 SER A 137 ASP A 141 5 5 HELIX 7 AA7 PRO A 181 LEU A 190 1 10 HELIX 8 AA8 PRO A 191 LEU A 193 5 3 HELIX 9 AA9 GLY A 199 PHE A 207 1 9 HELIX 10 AB1 SER A 215 ASP A 231 1 17 HELIX 11 AB2 ASP A 231 SER A 238 1 8 HELIX 12 AB3 LYS A 276 LEU A 280 5 5 HELIX 13 AB4 HIS A 282 LYS A 285 5 4 HELIX 14 AB5 SER A 286 ASN A 296 1 11 SHEET 1 AA1 8 ILE A 13 GLN A 15 0 SHEET 2 AA1 8 VAL A 42 PHE A 45 1 O PHE A 44 N ILE A 14 SHEET 3 AA1 8 THR A 250 PHE A 254 -1 O THR A 250 N PHE A 45 SHEET 4 AA1 8 ARG A 159 ASN A 166 -1 N PHE A 164 O TRP A 251 SHEET 5 AA1 8 LEU A 268 LEU A 275 -1 O LEU A 275 N ARG A 159 SHEET 6 AA1 8 LYS A 120 ARG A 127 -1 N SER A 125 O GLU A 270 SHEET 7 AA1 8 ILE A 71 ASP A 74 -1 N TYR A 73 O THR A 124 SHEET 8 AA1 8 THR A 79 LYS A 81 -1 O LYS A 81 N SER A 72 SHEET 1 AA2 3 VAL A 241 PHE A 245 0 SHEET 2 AA2 3 ARG A 174 ILE A 178 -1 N ARG A 174 O PHE A 245 SHEET 3 AA2 3 HIS A 260 LYS A 264 -1 O ASP A 263 N SER A 175 LINK NE2 HIS A 146 FE FE A 401 1555 1555 2.28 LINK OD1 ASP A 148 FE FE A 401 1555 1555 2.07 LINK NE2 HIS A 260 FE FE A 401 1555 1555 2.22 LINK FE FE A 401 O1 AKG A 402 1555 1555 2.11 LINK FE FE A 401 O5 AKG A 402 1555 1555 2.20 LINK FE FE A 401 O HOH A 582 1555 1555 2.22 SITE 1 AC1 5 HIS A 146 ASP A 148 HIS A 260 AKG A 402 SITE 2 AC1 5 HOH A 582 SITE 1 AC2 12 ARG A 127 ASP A 142 HIS A 146 ASP A 148 SITE 2 AC2 12 ARG A 162 PHE A 164 ARG A 174 TRP A 176 SITE 3 AC2 12 HIS A 260 VAL A 262 FE A 401 HOH A 514 SITE 1 AC3 6 GLY A 40 GLY A 179 GLU A 180 VAL A 258 SITE 2 AC3 6 LEU A 259 HOH A 548 SITE 1 AC4 9 ILE A 178 GLY A 179 LEU A 193 TYR A 220 SITE 2 AC4 9 GLN A 240 VAL A 241 LEU A 295 HOH A 552 SITE 3 AC4 9 HOH A 612 SITE 1 AC5 2 GLY A 212 TYR A 213 SITE 1 AC6 4 LEU A 57 PHE A 202 TYR A 205 HOH A 517 SITE 1 AC7 8 ARG A 76 ALA A 122 ARG A 123 SER A 153 SITE 2 AC7 8 PRO A 154 ILE A 160 ARG A 162 HIS A 274 SITE 1 AC8 2 ARG A 214 LEU A 222 SITE 1 AC9 6 THR A 79 LYS A 81 LYS A 276 ASN A 278 SITE 2 AC9 6 SER A 304 HOH A 599 CRYST1 45.710 59.204 116.264 90.00 90.00 90.00 P 21 21 21 4 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 0.021877 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016891 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008601 0.00000