HEADER BIOSYNTHETIC PROTEIN 28-NOV-17 5YW0 TITLE CRYSTAL STRUCTURE OF THE KDO HYDROXYLASE KDOO, A NON-HEME FE(II) TITLE 2 ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE IN COMPLEX WITH SUCCINATE TITLE 3 AND FE(III) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN KDOO; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID HYDROXYLASE,KDO COMPND 5 HYDROXYLASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLACIDIPHILUM INFERNORUM; 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 27-MAR-24 5YW0 1 LINK REVDAT 2 24-OCT-18 5YW0 1 JRNL REVDAT 1 05-SEP-18 5YW0 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. 1.49 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 50204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2501 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 23.5387 - 3.8927 0.99 2966 155 0.1665 0.1574 REMARK 3 2 3.8927 - 3.0920 1.00 2853 150 0.1539 0.1599 REMARK 3 3 3.0920 - 2.7018 0.99 2793 144 0.1775 0.1966 REMARK 3 4 2.7018 - 2.4551 0.99 2799 149 0.1692 0.1988 REMARK 3 5 2.4551 - 2.2792 1.00 2756 146 0.1683 0.1962 REMARK 3 6 2.2792 - 2.1450 0.99 2769 144 0.1604 0.2082 REMARK 3 7 2.1450 - 2.0376 0.98 2720 143 0.1581 0.1733 REMARK 3 8 2.0376 - 1.9489 0.99 2727 139 0.1570 0.1725 REMARK 3 9 1.9489 - 1.8740 0.98 2705 141 0.1557 0.1800 REMARK 3 10 1.8740 - 1.8093 0.97 2698 144 0.1644 0.2006 REMARK 3 11 1.8093 - 1.7528 0.97 2656 141 0.1609 0.2092 REMARK 3 12 1.7528 - 1.7027 0.96 2661 142 0.1655 0.1974 REMARK 3 13 1.7027 - 1.6579 0.96 2639 140 0.1696 0.1914 REMARK 3 14 1.6579 - 1.6174 0.95 2618 135 0.1715 0.1774 REMARK 3 15 1.6174 - 1.5807 0.94 2561 132 0.1841 0.2235 REMARK 3 16 1.5807 - 1.5470 0.89 2453 130 0.2031 0.2444 REMARK 3 17 1.5470 - 1.5161 0.84 2272 121 0.2193 0.2454 REMARK 3 18 1.5161 - 1.4875 0.75 2057 105 0.2388 0.2629 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) : 18.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.17 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 2505 REMARK 3 ANGLE : 0.790 3367 REMARK 3 CHIRALITY : 0.079 356 REMARK 3 PLANARITY : 0.005 433 REMARK 3 DIHEDRAL : 17.114 953 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): -3.1390 3.2664 -6.1735 REMARK 3 T TENSOR REMARK 3 T11: 0.1074 T22: 0.1130 REMARK 3 T33: 0.1267 T12: 0.0027 REMARK 3 T13: 0.0208 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 1.7168 L22: 2.3243 REMARK 3 L33: 2.5045 L12: 0.5318 REMARK 3 L13: 0.9840 L23: 0.4863 REMARK 3 S TENSOR REMARK 3 S11: -0.0192 S12: -0.1017 S13: 0.0834 REMARK 3 S21: 0.1730 S22: -0.0232 S23: -0.1264 REMARK 3 S31: -0.1086 S32: 0.0432 S33: 0.0443 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 128 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4145 -3.7649 -17.7587 REMARK 3 T TENSOR REMARK 3 T11: 0.1980 T22: 0.2582 REMARK 3 T33: 0.3730 T12: 0.0049 REMARK 3 T13: -0.0066 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.0072 L22: 2.3645 REMARK 3 L33: 3.6944 L12: 0.0360 REMARK 3 L13: -0.0737 L23: 2.1915 REMARK 3 S TENSOR REMARK 3 S11: 0.1108 S12: -0.0406 S13: 0.0217 REMARK 3 S21: -0.0088 S22: 0.1533 S23: -1.0379 REMARK 3 S31: 0.0047 S32: 0.6150 S33: -0.2281 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 307 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9283 -11.5436 -17.1170 REMARK 3 T TENSOR REMARK 3 T11: 0.0946 T22: 0.1118 REMARK 3 T33: 0.0918 T12: 0.0026 REMARK 3 T13: -0.0005 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.5669 L22: 1.6401 REMARK 3 L33: 0.9663 L12: -0.0590 REMARK 3 L13: 0.0460 L23: 0.1686 REMARK 3 S TENSOR REMARK 3 S11: 0.0482 S12: 0.0348 S13: -0.0302 REMARK 3 S21: 0.0164 S22: -0.0420 S23: -0.0593 REMARK 3 S31: 0.1282 S32: 0.0486 S33: -0.0083 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 5YW0 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_1300006004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-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 : 50288 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 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 (%) : 95.5 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.45600 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: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.37 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 22.85800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.09000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.63700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.09000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.85800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.63700 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: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 ALA A 68 REMARK 465 LYS A 69 REMARK 465 ALA A 135 REMARK 465 THR A 136 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 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 LEU A 307 CG CD1 CD2 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 O2 SIN A 408 O HOH A 501 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 19 NZ LYS A 86 4455 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 303 CD GLU A 303 OE2 -0.078 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 -142.90 -125.56 REMARK 500 PHE A 267 93.82 83.91 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 401 REMARK 610 PG4 A 402 REMARK 610 PG4 A 403 REMARK 610 PG4 A 404 REMARK 610 PG4 A 405 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 406 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 146 NE2 REMARK 620 2 ASP A 148 OD1 94.5 REMARK 620 3 HIS A 260 NE2 87.9 95.1 REMARK 620 4 SIN A 408 O1 90.8 172.9 89.8 REMARK 620 5 HOH A 501 O 173.2 85.7 85.3 89.7 REMARK 620 6 HOH A 509 O 82.9 84.3 170.7 91.7 103.9 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 PG4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 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 FE A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SIN A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 412 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5YVZ 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 FE(III) 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 5YW0 A 1 305 UNP B3DUR4 B3DUR4_METI4 1 305 SEQADV 5YW0 LYS A 306 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 LEU A 307 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 ALA A 308 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 ALA A 309 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 ALA A 310 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 LEU A 311 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 GLU A 312 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 HIS A 313 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 HIS A 314 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 HIS A 315 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 HIS A 316 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 HIS A 317 UNP B3DUR4 EXPRESSION TAG SEQADV 5YW0 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 PG4 A 401 10 HET PG4 A 402 7 HET PG4 A 403 7 HET PG4 A 404 10 HET PG4 A 405 7 HET FE A 406 1 HET GOL A 407 6 HET SIN A 408 8 HET ACT A 409 4 HET ACT A 410 4 HET ACT A 411 4 HET ACT A 412 4 HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM FE FE (III) ION HETNAM GOL GLYCEROL HETNAM SIN SUCCINIC ACID HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PG4 5(C8 H18 O5) FORMUL 7 FE FE 3+ FORMUL 8 GOL C3 H8 O3 FORMUL 9 SIN C4 H6 O4 FORMUL 10 ACT 4(C2 H3 O2 1-) FORMUL 14 HOH *221(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 PRO A 181 LEU A 190 1 10 HELIX 7 AA7 PRO A 191 LEU A 193 5 3 HELIX 8 AA8 GLY A 199 PHE A 207 1 9 HELIX 9 AA9 SER A 215 ASP A 231 1 17 HELIX 10 AB1 ASP A 231 SER A 238 1 8 HELIX 11 AB2 LYS A 276 LEU A 280 5 5 HELIX 12 AB3 HIS A 282 LYS A 285 5 4 HELIX 13 AB4 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 VAL A 42 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 ALA A 122 O THR A 272 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 TRP A 176 O PHE A 243 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 406 1555 1555 2.29 LINK OD1 ASP A 148 FE FE A 406 1555 1555 2.13 LINK NE2 HIS A 260 FE FE A 406 1555 1555 2.19 LINK FE FE A 406 O1 SIN A 408 1555 1555 2.15 LINK FE FE A 406 O HOH A 501 1555 1555 2.50 LINK FE FE A 406 O HOH A 509 1555 1555 2.07 SITE 1 AC1 7 GLY A 179 LEU A 193 TYR A 220 GLN A 240 SITE 2 AC1 7 VAL A 241 LEU A 295 HOH A 574 SITE 1 AC2 3 HIS A 109 TYR A 205 HOH A 627 SITE 1 AC3 7 ARG A 76 ALA A 122 ARG A 123 ARG A 162 SITE 2 AC3 7 THR A 272 HIS A 274 HOH A 513 SITE 1 AC4 2 TYR A 213 HOH A 505 SITE 1 AC5 1 GLN A 15 SITE 1 AC6 6 HIS A 146 ASP A 148 HIS A 260 SIN A 408 SITE 2 AC6 6 HOH A 501 HOH A 509 SITE 1 AC7 7 PRO A 12 GLY A 40 GLY A 179 GLU A 180 SITE 2 AC7 7 VAL A 258 LEU A 259 HOH A 553 SITE 1 AC8 13 ARG A 127 ASP A 142 HIS A 146 ARG A 162 SITE 2 AC8 13 ARG A 174 TRP A 176 HIS A 260 VAL A 262 SITE 3 AC8 13 FE A 406 ACT A 409 HOH A 501 HOH A 509 SITE 4 AC8 13 HOH A 510 SITE 1 AC9 4 PHE A 150 ARG A 162 SIN A 408 HOH A 509 SITE 1 AD1 5 GLY A 156 LEU A 288 GLU A 303 HOH A 503 SITE 2 AD1 5 HOH A 514 SITE 1 AD2 1 ARG A 214 SITE 1 AD3 4 LYS A 276 ASN A 278 SER A 304 HOH A 514 CRYST1 45.716 59.274 116.180 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 0.021874 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008607 0.00000