HEADER BIOSYNTHETIC PROTEIN 12-OCT-17 5YKA TITLE CRYSTAL STRUCTURE OF THE KDO HYDROXYLASE KDOO, A NON-HEME FE(II) TITLE 2 ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE IN COMPLEX WITH COBALT(II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN KDOO; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KDO HYDROXYLASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLACIDIPHILUM INFERNORUM (ISOLATE V4); SOURCE 3 ORGANISM_TAXID: 481448; SOURCE 4 STRAIN: ISOLATE V4; 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 5YKA 1 REMARK LINK REVDAT 2 24-OCT-18 5YKA 1 JRNL REVDAT 1 05-SEP-18 5YKA 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 57358 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2865 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 23.6415 - 3.9237 1.00 2936 155 0.1576 0.1784 REMARK 3 2 3.9237 - 3.1166 1.00 2812 147 0.1425 0.1672 REMARK 3 3 3.1166 - 2.7233 1.00 2778 147 0.1678 0.2028 REMARK 3 4 2.7233 - 2.4746 1.00 2767 145 0.1581 0.1797 REMARK 3 5 2.4746 - 2.2974 1.00 2746 145 0.1610 0.1690 REMARK 3 6 2.2974 - 2.1620 1.00 2737 144 0.1567 0.1698 REMARK 3 7 2.1620 - 2.0538 1.00 2746 143 0.1516 0.1826 REMARK 3 8 2.0538 - 1.9644 1.00 2720 145 0.1495 0.1732 REMARK 3 9 1.9644 - 1.8889 1.00 2739 143 0.1491 0.1549 REMARK 3 10 1.8889 - 1.8237 1.00 2689 141 0.1550 0.1694 REMARK 3 11 1.8237 - 1.7667 1.00 2716 143 0.1489 0.1733 REMARK 3 12 1.7667 - 1.7162 1.00 2712 143 0.1488 0.1595 REMARK 3 13 1.7162 - 1.6710 1.00 2711 142 0.1472 0.1653 REMARK 3 14 1.6710 - 1.6303 1.00 2689 143 0.1549 0.1920 REMARK 3 15 1.6303 - 1.5932 1.00 2720 143 0.1585 0.1733 REMARK 3 16 1.5932 - 1.5593 1.00 2689 141 0.1585 0.2040 REMARK 3 17 1.5593 - 1.5281 1.00 2683 141 0.1816 0.2018 REMARK 3 18 1.5281 - 1.4993 1.00 2717 144 0.1816 0.2196 REMARK 3 19 1.4993 - 1.4725 1.00 2682 141 0.1897 0.2140 REMARK 3 20 1.4725 - 1.4476 0.92 2504 129 0.2083 0.2419 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.83 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 2583 REMARK 3 ANGLE : 0.816 3478 REMARK 3 CHIRALITY : 0.081 371 REMARK 3 PLANARITY : 0.006 440 REMARK 3 DIHEDRAL : 17.866 982 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 127 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.5531 3.1779 -5.9605 REMARK 3 T TENSOR REMARK 3 T11: 0.0980 T22: 0.1052 REMARK 3 T33: 0.1066 T12: -0.0004 REMARK 3 T13: 0.0101 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 1.5359 L22: 2.0225 REMARK 3 L33: 2.1816 L12: 0.3316 REMARK 3 L13: 0.6602 L23: 0.3780 REMARK 3 S TENSOR REMARK 3 S11: -0.0018 S12: -0.1272 S13: 0.0869 REMARK 3 S21: 0.1817 S22: -0.0337 S23: -0.1099 REMARK 3 S31: -0.0916 S32: 0.0513 S33: 0.0307 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 128 THROUGH 307 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.1798 -10.9078 -17.2658 REMARK 3 T TENSOR REMARK 3 T11: 0.0839 T22: 0.1009 REMARK 3 T33: 0.0831 T12: 0.0046 REMARK 3 T13: -0.0047 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.5238 L22: 1.5939 REMARK 3 L33: 0.8414 L12: -0.1421 REMARK 3 L13: 0.0313 L23: 0.2692 REMARK 3 S TENSOR REMARK 3 S11: 0.0399 S12: 0.0357 S13: -0.0178 REMARK 3 S21: 0.0177 S22: -0.0327 S23: -0.1030 REMARK 3 S31: 0.1001 S32: 0.0723 S33: -0.0033 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 5YKA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005260. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : SI(111) 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 : 57453 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.448 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.45400 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 (%): 43.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE (PH 4.5), 200MM REMARK 280 LITHIUM SULFATE, 50% V/V PEG 400, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 22.90100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.21900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.80350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.21900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.90100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.80350 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: 4100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 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 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 ARG A 134 CD NE CZ NH1 NH2 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 ARG A 134 CG 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 OXT ACT A 417 O HOH A 501 2.02 REMARK 500 O HOH A 634 O HOH A 677 2.10 REMARK 500 O HOH A 560 O HOH A 647 2.12 REMARK 500 O HOH A 576 O HOH A 633 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 253 CB - CA - C ANGL. DEV. = -11.8 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 ALA A 122 -142.37 -124.60 REMARK 500 PHE A 267 95.84 83.19 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 A 774 DISTANCE = 5.92 ANGSTROMS 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 407 REMARK 610 PG4 A 408 REMARK 610 PG4 A 409 REMARK 610 PG4 A 410 REMARK 610 PG4 A 411 REMARK 610 PG4 A 412 REMARK 610 PG4 A 413 REMARK 610 PG4 A 414 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 401 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 146 NE2 REMARK 620 2 ASP A 148 OD1 93.6 REMARK 620 3 HIS A 260 NE2 89.7 92.9 REMARK 620 4 HOH A 534 O 177.1 89.3 90.7 REMARK 620 5 HOH A 536 O 89.3 85.2 177.8 90.4 REMARK 620 6 HOH A 623 O 91.9 171.8 93.1 85.2 88.9 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 CO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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 PG4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 420 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5Y7S RELATED DB: PDB REMARK 900 5Y7S CONTAINS THE SAME PROTEIN (APO) REMARK 900 RELATED ID: 5Y9X RELATED DB: PDB REMARK 900 5Y9X CONTAINS THE SAME PROETIN IN COMPLEX WITH COBALT(II) AND REMARK 900 ALPHAKETOGLUTARATE REMARK 900 RELATED ID: 5Y9Y RELATED DB: PDB REMARK 900 5Y9Y CONTAINS THE SAME PROTEIN IN COMPLEX WITH COBALT(II) AND REMARK 900 SUCCINATE DBREF 5YKA A 1 305 UNP B3DUR4 B3DUR4_METI4 1 305 SEQADV 5YKA LYS A 306 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA LEU A 307 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA ALA A 308 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA ALA A 309 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA ALA A 310 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA LEU A 311 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA GLU A 312 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA HIS A 313 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA HIS A 314 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA HIS A 315 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA HIS A 316 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA HIS A 317 UNP B3DUR4 EXPRESSION TAG SEQADV 5YKA 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 CO A 401 1 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET GOL A 406 6 HET PG4 A 407 7 HET PG4 A 408 11 HET PG4 A 409 20 HET PG4 A 410 4 HET PG4 A 411 4 HET PG4 A 412 7 HET PG4 A 413 7 HET PG4 A 414 4 HET ACT A 415 4 HET ACT A 416 4 HET ACT A 417 4 HET ACT A 418 4 HET CL A 419 1 HET CL A 420 1 HETNAM CO COBALT (II) ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CO CO 2+ FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 GOL C3 H8 O3 FORMUL 8 PG4 8(C8 H18 O5) FORMUL 16 ACT 4(C2 H3 O2 1-) FORMUL 20 CL 2(CL 1-) FORMUL 22 HOH *274(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 GLU A 130 ARG A 134 5 5 HELIX 7 AA7 SER A 137 ASP A 141 5 5 HELIX 8 AA8 PRO A 181 LEU A 190 1 10 HELIX 9 AA9 PRO A 191 LEU A 193 5 3 HELIX 10 AB1 GLY A 199 PHE A 207 1 9 HELIX 11 AB2 SER A 215 ASP A 231 1 17 HELIX 12 AB3 ASP A 231 SER A 238 1 8 HELIX 13 AB4 LYS A 276 LEU A 280 5 5 HELIX 14 AB5 HIS A 282 LYS A 285 5 4 HELIX 15 AB6 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 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 CO CO A 401 1555 1555 2.15 LINK OD1 ASP A 148 CO CO A 401 1555 1555 2.12 LINK NE2 HIS A 260 CO CO A 401 1555 1555 2.17 LINK CO CO A 401 O HOH A 534 1555 1555 2.12 LINK CO CO A 401 O HOH A 536 1555 1555 2.13 LINK CO CO A 401 O HOH A 623 1555 1555 2.20 SITE 1 AC1 6 HIS A 146 ASP A 148 HIS A 260 HOH A 534 SITE 2 AC1 6 HOH A 536 HOH A 623 SITE 1 AC2 5 ARG A 127 PHE A 150 ARG A 162 HOH A 536 SITE 2 AC2 5 HOH A 574 SITE 1 AC3 7 THR A 79 LYS A 81 LYS A 276 ASN A 278 SITE 2 AC3 7 SER A 304 HOH A 629 HOH A 654 SITE 1 AC4 2 PRO A 75 ARG A 76 SITE 1 AC5 4 ARG A 76 ALA A 122 HIS A 274 HOH A 665 SITE 1 AC6 9 PRO A 12 GLY A 40 GLY A 179 GLU A 180 SITE 2 AC6 9 VAL A 258 LEU A 259 HOH A 558 HOH A 601 SITE 3 AC6 9 HOH A 664 SITE 1 AC7 4 PRO A 151 SER A 152 ILE A 209 ARG A 214 SITE 1 AC8 10 ILE A 178 GLY A 179 LEU A 193 TYR A 220 SITE 2 AC8 10 GLN A 240 VAL A 241 LYS A 297 HOH A 582 SITE 3 AC8 10 HOH A 588 HOH A 699 SITE 1 AC9 5 ALA A 106 HIS A 109 LEU A 110 TYR A 205 SITE 2 AC9 5 HOH A 547 SITE 1 AD1 7 GLY A 156 GLY A 157 LYS A 276 VAL A 277 SITE 2 AD1 7 HOH A 555 HOH A 629 HOH A 654 SITE 1 AD2 7 ARG A 201 SER A 215 LEU A 216 LEU A 299 SITE 2 AD2 7 SER A 301 HOH A 578 HOH A 670 SITE 1 AD3 2 TYR A 213 HOH A 505 SITE 1 AD4 2 ARG A 177 ASP A 263 SITE 1 AD5 5 PHE A 164 ARG A 174 TRP A 176 VAL A 262 SITE 2 AD5 5 LEU A 268 SITE 1 AD6 3 PHE A 150 PRO A 151 SER A 152 SITE 1 AD7 2 GLU A 292 HOH A 501 SITE 1 AD8 6 PRO A 154 THR A 155 GLY A 156 LYS A 211 SITE 2 AD8 6 HOH A 505 HOH A 507 SITE 1 AD9 3 GLY A 199 PHE A 202 TYR A 213 SITE 1 AE1 5 PHE A 16 ASP A 17 ILE A 29 HOH A 693 SITE 2 AE1 5 HOH A 723 CRYST1 45.802 59.607 116.438 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 0.021833 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008588 0.00000