HEADER OXIDOREDUCTASE 03-JUL-13 4LIT TITLE STRUCTURE OF YCFD A RIBOSOMAL OXYGENASE FROM ESCHERICHIA COLI IN TITLE 2 COMPLEX WITH COBALT AND 2-OXOGLUTARATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBOSOMAL OXYGENASE YCFD, ROX; COMPND 5 EC: 1.14.11.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B1128, JW1114, YCFD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834S; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS JMJC DOMAIN, DIOXYGENASE, HYDROXYLATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.C.BRISSETT,A.J.DOHERTY REVDAT 4 20-SEP-23 4LIT 1 REMARK SEQADV LINK REVDAT 3 09-JUL-14 4LIT 1 JRNL REVDAT 2 25-JUN-14 4LIT 1 JRNL REVDAT 1 14-MAY-14 4LIT 0 JRNL AUTH R.CHOWDHURY,R.SEKIRNIK,N.C.BRISSETT,T.KROJER,C.H.HO,S.S.NG, JRNL AUTH 2 I.J.CLIFTON,W.GE,N.J.KERSHAW,G.C.FOX,J.R.MUNIZ,M.VOLLMAR, JRNL AUTH 3 C.PHILLIPS,E.S.PILKA,K.L.KAVANAGH,F.VON DELFT,U.OPPERMANN, JRNL AUTH 4 M.A.MCDONOUGH,A.J.DOHERTY,C.J.SCHOFIELD JRNL TITL RIBOSOMAL OXYGENASES ARE STRUCTURALLY CONSERVED FROM JRNL TITL 2 PROKARYOTES TO HUMANS. JRNL REF NATURE V. 509 422 2014 JRNL REFN ISSN 0028-0836 JRNL PMID 24814345 JRNL DOI 10.1038/NATURE13263 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43461 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 2240 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.67 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 : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 36:83) REMARK 3 ORIGIN FOR THE GROUP (A): 26.0979 51.5517 72.9587 REMARK 3 T TENSOR REMARK 3 T11: 0.2848 T22: 0.2327 REMARK 3 T33: 0.2375 T12: 0.0350 REMARK 3 T13: 0.0077 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 3.5983 L22: 3.6124 REMARK 3 L33: 3.3901 L12: 1.3514 REMARK 3 L13: -0.1508 L23: 0.2039 REMARK 3 S TENSOR REMARK 3 S11: -0.0425 S12: -0.0077 S13: 0.1277 REMARK 3 S21: -0.0977 S22: 0.1036 S23: 0.0683 REMARK 3 S31: -0.1200 S32: -0.0112 S33: -0.0696 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 84:129) REMARK 3 ORIGIN FOR THE GROUP (A): 44.0972 57.9704 73.7943 REMARK 3 T TENSOR REMARK 3 T11: 0.3682 T22: 0.4967 REMARK 3 T33: 0.3873 T12: -0.1141 REMARK 3 T13: 0.0503 T23: -0.0373 REMARK 3 L TENSOR REMARK 3 L11: 3.2642 L22: 3.4342 REMARK 3 L33: 4.3975 L12: -0.2800 REMARK 3 L13: -1.0665 L23: 0.2305 REMARK 3 S TENSOR REMARK 3 S11: 0.0452 S12: -0.1979 S13: 0.4960 REMARK 3 S21: -0.2123 S22: 0.1703 S23: -0.6311 REMARK 3 S31: -0.3140 S32: 1.0927 S33: -0.1998 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 130:141) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0149 50.0176 82.9415 REMARK 3 T TENSOR REMARK 3 T11: 0.3684 T22: 0.2737 REMARK 3 T33: 0.2521 T12: 0.0806 REMARK 3 T13: -0.0049 T23: -0.0359 REMARK 3 L TENSOR REMARK 3 L11: 5.5486 L22: 4.1209 REMARK 3 L33: 2.3914 L12: 2.8778 REMARK 3 L13: -0.7420 L23: -2.8303 REMARK 3 S TENSOR REMARK 3 S11: 0.0143 S12: -0.0872 S13: 0.3726 REMARK 3 S21: 0.5471 S22: -0.2165 S23: 0.0986 REMARK 3 S31: -0.6633 S32: -0.1587 S33: 0.1094 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 142:236) REMARK 3 ORIGIN FOR THE GROUP (A): 35.2097 46.1205 69.9054 REMARK 3 T TENSOR REMARK 3 T11: 0.2773 T22: 0.2885 REMARK 3 T33: 0.2823 T12: 0.0239 REMARK 3 T13: 0.0281 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 3.6330 L22: 3.1578 REMARK 3 L33: 4.8175 L12: 1.4928 REMARK 3 L13: -0.6239 L23: 0.8657 REMARK 3 S TENSOR REMARK 3 S11: -0.1428 S12: 0.1808 S13: -0.1793 REMARK 3 S21: -0.0686 S22: 0.1952 S23: -0.2081 REMARK 3 S31: 0.1836 S32: 0.4826 S33: -0.0366 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 237:293) REMARK 3 ORIGIN FOR THE GROUP (A): 36.3898 31.2621 110.7328 REMARK 3 T TENSOR REMARK 3 T11: 0.2533 T22: 0.3059 REMARK 3 T33: 0.2811 T12: 0.0159 REMARK 3 T13: -0.0407 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.4195 L22: 1.3647 REMARK 3 L33: 3.7134 L12: -0.8044 REMARK 3 L13: 1.0209 L23: -2.0596 REMARK 3 S TENSOR REMARK 3 S11: -0.0222 S12: -0.1164 S13: 0.0170 REMARK 3 S21: 0.0815 S22: 0.1359 S23: -0.0592 REMARK 3 S31: -0.1071 S32: -0.2293 S33: -0.1157 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 294:355) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5716 58.8204 97.6663 REMARK 3 T TENSOR REMARK 3 T11: 0.4035 T22: 0.3454 REMARK 3 T33: 0.2982 T12: 0.0894 REMARK 3 T13: 0.0194 T23: -0.0292 REMARK 3 L TENSOR REMARK 3 L11: 2.1562 L22: 2.5501 REMARK 3 L33: 1.7788 L12: -1.2911 REMARK 3 L13: 0.4917 L23: 0.2615 REMARK 3 S TENSOR REMARK 3 S11: -0.2103 S12: -0.3504 S13: -0.1022 REMARK 3 S21: 0.2345 S22: 0.3597 S23: -0.0054 REMARK 3 S31: 0.1471 S32: 0.2103 S33: -0.1378 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 356:378) REMARK 3 ORIGIN FOR THE GROUP (A): 15.9863 57.9647 97.9880 REMARK 3 T TENSOR REMARK 3 T11: 0.3579 T22: 0.2458 REMARK 3 T33: 0.3541 T12: -0.0414 REMARK 3 T13: -0.0206 T23: -0.0469 REMARK 3 L TENSOR REMARK 3 L11: 3.0869 L22: 2.3274 REMARK 3 L33: 3.3425 L12: -2.4467 REMARK 3 L13: -1.3574 L23: 0.0319 REMARK 3 S TENSOR REMARK 3 S11: 0.0462 S12: -0.1358 S13: -0.1647 REMARK 3 S21: -0.0340 S22: -0.0137 S23: 0.2152 REMARK 3 S31: 0.2716 S32: -0.2026 S33: 0.1004 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 379:407) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9696 66.2739 99.2486 REMARK 3 T TENSOR REMARK 3 T11: 0.3327 T22: 0.2539 REMARK 3 T33: 0.2755 T12: 0.0367 REMARK 3 T13: -0.0094 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 2.5279 L22: 1.4240 REMARK 3 L33: 2.6540 L12: -0.2191 REMARK 3 L13: -0.0795 L23: 0.8584 REMARK 3 S TENSOR REMARK 3 S11: 0.1436 S12: -0.0086 S13: -0.0188 REMARK 3 S21: 0.1202 S22: -0.0235 S23: 0.0077 REMARK 3 S31: 0.1737 S32: 0.0930 S33: -0.0875 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 4LIT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080682. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 : VARIMAX HF REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23748 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 69.869 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.16400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.60 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : 0.73000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.2 REMARK 200 STARTING MODEL: PDB ENTRY 4LIU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM COBALT CHLORIDE, 50MM 2 REMARK 280 -OXOGLUTARATE PH 4.2, 1.5M 1,6 HEXANEDIOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 285K, PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 104.43000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.07000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 156.64500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.07000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.07000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.21500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.07000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.07000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 156.64500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.07000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.07000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.21500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 104.43000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 208.86000 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 MET A 21 REMARK 465 ALA A 22 REMARK 465 SER A 23 REMARK 465 MET A 24 REMARK 465 THR A 25 REMARK 465 GLY A 26 REMARK 465 GLY A 27 REMARK 465 GLU A 28 REMARK 465 GLU A 29 REMARK 465 MET A 30 REMARK 465 GLY A 31 REMARK 465 ARG A 32 REMARK 465 GLY A 33 REMARK 465 SER A 34 REMARK 465 MET A 35 REMARK 465 GLN A 183 REMARK 465 MET A 184 REMARK 465 LYS A 185 REMARK 465 GLN A 186 REMARK 465 HIS A 187 REMARK 465 CYS A 188 REMARK 465 PRO A 189 REMARK 465 HIS A 190 REMARK 465 PRO A 191 REMARK 465 ASP A 192 REMARK 465 LEU A 193 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 GLU A 36 CG CD OE1 OE2 REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 ASP A 106 CG OD1 OD2 REMARK 470 HIS A 107 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 194 CG CD1 CD2 REMARK 470 GLN A 195 CG CD OE1 NE2 REMARK 470 GLN A 254 CG CD OE1 NE2 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 712 O HOH A 713 2.00 REMARK 500 O HOH A 687 O HOH A 690 2.17 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 LYS A 53 -50.53 -137.63 REMARK 500 ASP A 106 -48.60 -28.16 REMARK 500 ASP A 143 -109.00 -104.39 REMARK 500 GLU A 406 -38.47 68.76 REMARK 500 REMARK 500 REMARK: NULL 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 501 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 159 NE2 REMARK 620 2 ASP A 161 OD2 112.1 REMARK 620 3 HIS A 221 NE2 90.3 85.7 REMARK 620 4 AKG A 502 O5 87.6 160.0 91.5 REMARK 620 5 AKG A 502 O2 82.4 104.3 169.2 80.4 REMARK 620 6 AKG A 502 C2 90.3 149.4 115.9 24.5 56.6 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LIU RELATED DB: PDB REMARK 900 SAME PROTEIN - APO FORM REMARK 900 RELATED ID: 4LIV RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH COBALT AND SUCCINIC ACID DBREF 4LIT A 35 407 UNP P27431 YCFD_ECOLI 1 373 SEQADV 4LIT MET A 1 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLY A 2 UNP P27431 EXPRESSION TAG SEQADV 4LIT SER A 3 UNP P27431 EXPRESSION TAG SEQADV 4LIT SER A 4 UNP P27431 EXPRESSION TAG SEQADV 4LIT HIS A 5 UNP P27431 EXPRESSION TAG SEQADV 4LIT HIS A 6 UNP P27431 EXPRESSION TAG SEQADV 4LIT HIS A 7 UNP P27431 EXPRESSION TAG SEQADV 4LIT HIS A 8 UNP P27431 EXPRESSION TAG SEQADV 4LIT HIS A 9 UNP P27431 EXPRESSION TAG SEQADV 4LIT HIS A 10 UNP P27431 EXPRESSION TAG SEQADV 4LIT SER A 11 UNP P27431 EXPRESSION TAG SEQADV 4LIT SER A 12 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLY A 13 UNP P27431 EXPRESSION TAG SEQADV 4LIT LEU A 14 UNP P27431 EXPRESSION TAG SEQADV 4LIT VAL A 15 UNP P27431 EXPRESSION TAG SEQADV 4LIT PRO A 16 UNP P27431 EXPRESSION TAG SEQADV 4LIT ARG A 17 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLY A 18 UNP P27431 EXPRESSION TAG SEQADV 4LIT SER A 19 UNP P27431 EXPRESSION TAG SEQADV 4LIT HIS A 20 UNP P27431 EXPRESSION TAG SEQADV 4LIT MET A 21 UNP P27431 EXPRESSION TAG SEQADV 4LIT ALA A 22 UNP P27431 EXPRESSION TAG SEQADV 4LIT SER A 23 UNP P27431 EXPRESSION TAG SEQADV 4LIT MET A 24 UNP P27431 EXPRESSION TAG SEQADV 4LIT THR A 25 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLY A 26 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLY A 27 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLU A 28 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLU A 29 UNP P27431 EXPRESSION TAG SEQADV 4LIT MET A 30 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLY A 31 UNP P27431 EXPRESSION TAG SEQADV 4LIT ARG A 32 UNP P27431 EXPRESSION TAG SEQADV 4LIT GLY A 33 UNP P27431 EXPRESSION TAG SEQADV 4LIT SER A 34 UNP P27431 EXPRESSION TAG SEQRES 1 A 407 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 407 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 407 GLY GLU GLU MET GLY ARG GLY SER MET GLU TYR GLN LEU SEQRES 4 A 407 THR LEU ASN TRP PRO ASP PHE LEU GLU ARG HIS TRP GLN SEQRES 5 A 407 LYS ARG PRO VAL VAL LEU LYS ARG GLY PHE ASN ASN PHE SEQRES 6 A 407 ILE ASP PRO ILE SER PRO ASP GLU LEU ALA GLY LEU ALA SEQRES 7 A 407 MET GLU SER GLU VAL ASP SER ARG LEU VAL SER HIS GLN SEQRES 8 A 407 ASP GLY LYS TRP GLN VAL SER HIS GLY PRO PHE GLU SER SEQRES 9 A 407 TYR ASP HIS LEU GLY GLU THR ASN TRP SER LEU LEU VAL SEQRES 10 A 407 GLN ALA VAL ASN HIS TRP HIS GLU PRO THR ALA ALA LEU SEQRES 11 A 407 MET ARG PRO PHE ARG GLU LEU PRO ASP TRP ARG ILE ASP SEQRES 12 A 407 ASP LEU MET ILE SER PHE SER VAL PRO GLY GLY GLY VAL SEQRES 13 A 407 GLY PRO HIS LEU ASP GLN TYR ASP VAL PHE ILE ILE GLN SEQRES 14 A 407 GLY THR GLY ARG ARG ARG TRP ARG VAL GLY GLU LYS LEU SEQRES 15 A 407 GLN MET LYS GLN HIS CYS PRO HIS PRO ASP LEU LEU GLN SEQRES 16 A 407 VAL ASP PRO PHE GLU ALA ILE ILE ASP GLU GLU LEU GLU SEQRES 17 A 407 PRO GLY ASP ILE LEU TYR ILE PRO PRO GLY PHE PRO HIS SEQRES 18 A 407 GLU GLY TYR ALA LEU GLU ASN ALA MET ASN TYR SER VAL SEQRES 19 A 407 GLY PHE ARG ALA PRO ASN THR ARG GLU LEU ILE SER GLY SEQRES 20 A 407 PHE ALA ASP TYR VAL LEU GLN ARG GLU LEU GLY GLY ASN SEQRES 21 A 407 TYR TYR SER ASP PRO ASP VAL PRO PRO ARG ALA HIS PRO SEQRES 22 A 407 ALA ASP VAL LEU PRO GLN GLU MET ASP LYS LEU ARG GLU SEQRES 23 A 407 MET MET LEU GLU LEU ILE ASN GLN PRO GLU HIS PHE LYS SEQRES 24 A 407 GLN TRP PHE GLY GLU PHE ILE SER GLN SER ARG HIS GLU SEQRES 25 A 407 LEU ASP ILE ALA PRO PRO GLU PRO PRO TYR GLN PRO ASP SEQRES 26 A 407 GLU ILE TYR ASP ALA LEU LYS GLN GLY GLU VAL LEU VAL SEQRES 27 A 407 ARG LEU GLY GLY LEU ARG VAL LEU ARG ILE GLY ASP ASP SEQRES 28 A 407 VAL TYR ALA ASN GLY GLU LYS ILE ASP SER PRO HIS ARG SEQRES 29 A 407 PRO ALA LEU ASP ALA LEU ALA SER ASN ILE ALA LEU THR SEQRES 30 A 407 ALA GLU ASN PHE GLY ASP ALA LEU GLU ASP PRO SER PHE SEQRES 31 A 407 LEU ALA MET LEU ALA ALA LEU VAL ASN SER GLY TYR TRP SEQRES 32 A 407 PHE PHE GLU GLY HET CO A 501 1 HET AKG A 502 10 HETNAM CO COBALT (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 CO CO 2+ FORMUL 3 AKG C5 H6 O5 FORMUL 4 HOH *137(H2 O) HELIX 1 1 ASN A 42 HIS A 50 1 9 HELIX 2 2 SER A 70 MET A 79 1 10 HELIX 3 3 ALA A 119 TRP A 123 5 5 HELIX 4 4 HIS A 124 ALA A 129 1 6 HELIX 5 5 LEU A 130 LEU A 137 5 8 HELIX 6 6 PRO A 138 TRP A 140 5 3 HELIX 7 7 ASN A 240 GLU A 256 1 17 HELIX 8 8 LEU A 277 ASN A 293 1 17 HELIX 9 9 GLN A 294 SER A 307 1 14 HELIX 10 10 GLN A 323 GLN A 333 1 11 HELIX 11 11 HIS A 363 ASN A 373 1 11 HELIX 12 12 THR A 377 GLY A 382 1 6 HELIX 13 13 ASP A 383 GLU A 386 5 4 HELIX 14 14 ASP A 387 SER A 400 1 14 SHEET 1 A 8 VAL A 56 LEU A 58 0 SHEET 2 A 8 ILE A 212 ILE A 215 -1 O ILE A 212 N LEU A 58 SHEET 3 A 8 VAL A 165 GLN A 169 -1 N ILE A 167 O LEU A 213 SHEET 4 A 8 ALA A 229 PHE A 236 -1 O TYR A 232 N ILE A 168 SHEET 5 A 8 ILE A 142 SER A 150 -1 N MET A 146 O SER A 233 SHEET 6 A 8 TRP A 113 VAL A 117 -1 N VAL A 117 O ILE A 147 SHEET 7 A 8 SER A 85 GLN A 91 -1 N ARG A 86 O LEU A 116 SHEET 8 A 8 LYS A 94 HIS A 99 -1 O GLN A 96 N SER A 89 SHEET 1 B 3 ALA A 201 LEU A 207 0 SHEET 2 B 3 ARG A 173 GLY A 179 -1 N VAL A 178 O ILE A 202 SHEET 3 B 3 HIS A 221 GLU A 227 -1 O LEU A 226 N ARG A 173 SHEET 1 C 3 ALA A 375 LEU A 376 0 SHEET 2 C 3 LEU A 337 ARG A 339 -1 N LEU A 337 O LEU A 376 SHEET 3 C 3 TRP A 403 PHE A 405 -1 O PHE A 404 N VAL A 338 SHEET 1 D 3 VAL A 345 ILE A 348 0 SHEET 2 D 3 ASP A 351 ALA A 354 -1 O ASP A 351 N ILE A 348 SHEET 3 D 3 GLU A 357 ILE A 359 -1 O GLU A 357 N ALA A 354 LINK NE2 HIS A 159 CO CO A 501 1555 1555 2.15 LINK OD2 ASP A 161 CO CO A 501 1555 1555 2.03 LINK NE2 HIS A 221 CO CO A 501 1555 1555 2.14 LINK CO CO A 501 O5 AKG A 502 1555 1555 2.13 LINK CO CO A 501 O2 AKG A 502 1555 1555 2.16 LINK CO CO A 501 C2 AKG A 502 1555 1555 2.77 CISPEP 1 GLY A 100 PRO A 101 0 1.97 CISPEP 2 GLU A 319 PRO A 320 0 1.95 SITE 1 AC1 4 HIS A 159 ASP A 161 HIS A 221 AKG A 502 SITE 1 AC2 10 MET A 146 SER A 148 HIS A 159 ASP A 161 SITE 2 AC2 10 ARG A 174 HIS A 221 CO A 501 HOH A 613 SITE 3 AC2 10 HOH A 615 HOH A 617 CRYST1 74.140 74.140 208.860 90.00 90.00 90.00 P 43 21 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 0.013488 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004788 0.00000