HEADER OXIDOREDUCTASE 03-JUL-13 4LIU TITLE STRUCTURE OF YCFD, A RIBOSOMAL OXYGENASE FROM ESCHERICHIA COLI. 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,G.C.FOX REVDAT 4 27-NOV-24 4LIU 1 REMARK SEQADV LINK REVDAT 3 09-JUL-14 4LIU 1 JRNL REVDAT 2 25-JUN-14 4LIU 1 JRNL REVDAT 1 14-MAY-14 4LIU 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. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 31369 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1590 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 43.0289 - 5.9999 0.98 2675 141 0.1983 0.2329 REMARK 3 2 5.9999 - 4.7643 0.99 2749 100 0.1732 0.2261 REMARK 3 3 4.7643 - 4.1626 1.00 2692 154 0.1475 0.1680 REMARK 3 4 4.1626 - 3.7822 1.00 2710 136 0.1581 0.2246 REMARK 3 5 3.7822 - 3.5113 1.00 2737 147 0.1898 0.2267 REMARK 3 6 3.5113 - 3.3043 1.00 2696 142 0.1921 0.2194 REMARK 3 7 3.3043 - 3.1389 1.00 2717 131 0.2173 0.2408 REMARK 3 8 3.1389 - 3.0023 1.00 2711 174 0.2622 0.3033 REMARK 3 9 3.0023 - 2.8868 1.00 2693 140 0.2700 0.2944 REMARK 3 10 2.8868 - 2.7872 1.00 2709 163 0.2753 0.3245 REMARK 3 11 2.7872 - 2.7000 0.99 2690 162 0.2948 0.3857 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.00 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 : 0.003 2989 REMARK 3 ANGLE : 0.807 4074 REMARK 3 CHIRALITY : 0.060 417 REMARK 3 PLANARITY : 0.003 545 REMARK 3 DIHEDRAL : 15.200 1099 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 35:39) REMARK 3 ORIGIN FOR THE GROUP (A): 22.2184 -18.4180 31.1742 REMARK 3 T TENSOR REMARK 3 T11: 0.4220 T22: 0.6123 REMARK 3 T33: 0.5195 T12: 0.2808 REMARK 3 T13: -0.0227 T23: -0.0357 REMARK 3 L TENSOR REMARK 3 L11: 8.4649 L22: 6.4569 REMARK 3 L33: 8.0058 L12: 4.8263 REMARK 3 L13: -2.9061 L23: 3.4402 REMARK 3 S TENSOR REMARK 3 S11: 0.5197 S12: -0.0361 S13: -1.5878 REMARK 3 S21: 0.4629 S22: 0.4337 S23: -1.5751 REMARK 3 S31: 0.6950 S32: 1.3202 S33: -0.3373 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 40:66) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8780 -16.1279 32.7988 REMARK 3 T TENSOR REMARK 3 T11: 0.2137 T22: 0.2149 REMARK 3 T33: 0.2479 T12: -0.0176 REMARK 3 T13: 0.0318 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 2.0525 L22: 1.8297 REMARK 3 L33: 3.6234 L12: 1.6540 REMARK 3 L13: -0.0359 L23: 0.3710 REMARK 3 S TENSOR REMARK 3 S11: -0.1184 S12: -0.1040 S13: -0.5186 REMARK 3 S21: -0.0773 S22: 0.1213 S23: -0.1254 REMARK 3 S31: 0.4798 S32: -0.3276 S33: -0.0097 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 67:99) REMARK 3 ORIGIN FOR THE GROUP (A): 22.8528 6.7613 30.4907 REMARK 3 T TENSOR REMARK 3 T11: 0.4289 T22: 0.4068 REMARK 3 T33: 0.3214 T12: -0.1473 REMARK 3 T13: -0.0006 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 3.9507 L22: 4.3546 REMARK 3 L33: 5.8428 L12: -0.3216 REMARK 3 L13: -1.5133 L23: 0.7294 REMARK 3 S TENSOR REMARK 3 S11: 0.2987 S12: -0.0161 S13: 0.5722 REMARK 3 S21: -0.7135 S22: 0.2688 S23: -0.4286 REMARK 3 S31: -1.2040 S32: 0.2107 S33: -0.3747 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 100:140) REMARK 3 ORIGIN FOR THE GROUP (A): 21.2648 -2.7954 27.3533 REMARK 3 T TENSOR REMARK 3 T11: 0.2950 T22: 0.3331 REMARK 3 T33: 0.2832 T12: -0.0639 REMARK 3 T13: 0.0458 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 2.7482 L22: 1.0759 REMARK 3 L33: 3.3930 L12: -0.8239 REMARK 3 L13: -0.2051 L23: 1.2178 REMARK 3 S TENSOR REMARK 3 S11: 0.1544 S12: 0.1338 S13: -0.0031 REMARK 3 S21: -0.2190 S22: 0.3220 S23: -0.7118 REMARK 3 S31: -0.4395 S32: 0.5838 S33: -0.2975 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 141:237) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7747 -2.3931 34.2245 REMARK 3 T TENSOR REMARK 3 T11: 0.2371 T22: 0.2115 REMARK 3 T33: 0.2064 T12: 0.0148 REMARK 3 T13: 0.0193 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 2.6185 L22: 3.0854 REMARK 3 L33: 3.8299 L12: 0.2839 REMARK 3 L13: 0.2857 L23: 0.8033 REMARK 3 S TENSOR REMARK 3 S11: 0.2355 S12: -0.1202 S13: 0.2226 REMARK 3 S21: 0.0909 S22: -0.1036 S23: 0.1016 REMARK 3 S31: -0.4809 S32: 0.0003 S33: -0.0758 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 238:290) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9257 0.4290 -7.0225 REMARK 3 T TENSOR REMARK 3 T11: 0.3184 T22: 0.2505 REMARK 3 T33: 0.2587 T12: 0.0395 REMARK 3 T13: 0.0362 T23: 0.0552 REMARK 3 L TENSOR REMARK 3 L11: 2.5272 L22: 1.6971 REMARK 3 L33: 4.0146 L12: -1.9131 REMARK 3 L13: 2.5990 L23: -1.2706 REMARK 3 S TENSOR REMARK 3 S11: 0.1498 S12: -0.1044 S13: 0.1086 REMARK 3 S21: -0.0623 S22: -0.0203 S23: -0.0209 REMARK 3 S31: 0.3718 S32: 0.1514 S33: -0.1460 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 291:310) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3666 -8.1959 3.0710 REMARK 3 T TENSOR REMARK 3 T11: 0.5192 T22: 0.5855 REMARK 3 T33: 0.3153 T12: 0.2390 REMARK 3 T13: 0.0292 T23: 0.1007 REMARK 3 L TENSOR REMARK 3 L11: 6.6771 L22: 2.4221 REMARK 3 L33: 2.0928 L12: -2.2660 REMARK 3 L13: 3.4256 L23: -1.9138 REMARK 3 S TENSOR REMARK 3 S11: 0.4664 S12: 1.0505 S13: -0.2876 REMARK 3 S21: -0.6465 S22: -0.2064 S23: -0.1092 REMARK 3 S31: 0.7230 S32: 0.7256 S33: -0.1914 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 311:360) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5488 -14.2774 7.4129 REMARK 3 T TENSOR REMARK 3 T11: 0.2050 T22: 0.2785 REMARK 3 T33: 0.2416 T12: 0.0539 REMARK 3 T13: 0.0445 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 3.0369 L22: 2.4343 REMARK 3 L33: 3.0410 L12: -2.1228 REMARK 3 L13: -0.6645 L23: -0.3080 REMARK 3 S TENSOR REMARK 3 S11: 0.2498 S12: 0.2143 S13: 0.2593 REMARK 3 S21: -0.2313 S22: -0.1207 S23: -0.1689 REMARK 3 S31: -0.1978 S32: -0.1323 S33: -0.1569 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 361:407) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1664 -20.6002 6.3548 REMARK 3 T TENSOR REMARK 3 T11: 0.2019 T22: 0.3240 REMARK 3 T33: 0.2335 T12: 0.0405 REMARK 3 T13: 0.0176 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 2.9065 L22: 4.4259 REMARK 3 L33: 2.0396 L12: -1.1196 REMARK 3 L13: -0.9207 L23: 0.1359 REMARK 3 S TENSOR REMARK 3 S11: 0.0248 S12: 0.0006 S13: -0.2149 REMARK 3 S21: -0.0378 S22: -0.1122 S23: 0.2876 REMARK 3 S31: 0.1875 S32: -0.0155 S33: 0.0912 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 4LIU 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_1000080683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17365 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 70.721 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.87200 REMARK 200 R SYM FOR SHELL (I) : 0.87200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS.HCL PH 7.5, 0.4M AMMONIUM REMARK 280 DIHYDROGEN PHOSPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 285K 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 104.97500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.55500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.55500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 157.46250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.55500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.55500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.48750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.55500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.55500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 157.46250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.55500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.55500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.48750 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 104.97500 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: 6930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 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 MSE 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 MSE A 21 REMARK 465 ALA A 22 REMARK 465 SER A 23 REMARK 465 MSE 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 MSE A 30 REMARK 465 GLY A 31 REMARK 465 ARG A 32 REMARK 465 GLY A 33 REMARK 465 SER A 34 REMARK 465 GLN A 183 REMARK 465 MSE 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 465 LEU A 194 REMARK 465 GLN A 195 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 60 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 91 CG CD OE1 NE2 REMARK 470 ASP A 92 CG OD1 OD2 REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 SER A 104 OG REMARK 470 ASP A 106 CG OD1 OD2 REMARK 470 HIS A 107 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 197 CG OD1 OD2 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 HIS A 50 -42.96 -133.59 REMARK 500 LYS A 53 -59.58 -129.58 REMARK 500 SER A 104 144.62 -170.09 REMARK 500 ASP A 106 -71.53 -43.05 REMARK 500 ASP A 143 -108.66 -118.68 REMARK 500 ASP A 266 52.70 -106.24 REMARK 500 GLU A 406 -66.59 64.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LIT RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH COBALT AND 2-OXOGLUTARATE REMARK 900 RELATED ID: 4LIV RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH COBALT AND SUCCINIC ACID DBREF 4LIU A 36 407 UNP P27431 YCFD_ECOLI 2 373 SEQADV 4LIU MSE A 1 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLY A 2 UNP P27431 EXPRESSION TAG SEQADV 4LIU SER A 3 UNP P27431 EXPRESSION TAG SEQADV 4LIU SER A 4 UNP P27431 EXPRESSION TAG SEQADV 4LIU HIS A 5 UNP P27431 EXPRESSION TAG SEQADV 4LIU HIS A 6 UNP P27431 EXPRESSION TAG SEQADV 4LIU HIS A 7 UNP P27431 EXPRESSION TAG SEQADV 4LIU HIS A 8 UNP P27431 EXPRESSION TAG SEQADV 4LIU HIS A 9 UNP P27431 EXPRESSION TAG SEQADV 4LIU HIS A 10 UNP P27431 EXPRESSION TAG SEQADV 4LIU SER A 11 UNP P27431 EXPRESSION TAG SEQADV 4LIU SER A 12 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLY A 13 UNP P27431 EXPRESSION TAG SEQADV 4LIU LEU A 14 UNP P27431 EXPRESSION TAG SEQADV 4LIU VAL A 15 UNP P27431 EXPRESSION TAG SEQADV 4LIU PRO A 16 UNP P27431 EXPRESSION TAG SEQADV 4LIU ARG A 17 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLY A 18 UNP P27431 EXPRESSION TAG SEQADV 4LIU SER A 19 UNP P27431 EXPRESSION TAG SEQADV 4LIU HIS A 20 UNP P27431 EXPRESSION TAG SEQADV 4LIU MSE A 21 UNP P27431 EXPRESSION TAG SEQADV 4LIU ALA A 22 UNP P27431 EXPRESSION TAG SEQADV 4LIU SER A 23 UNP P27431 EXPRESSION TAG SEQADV 4LIU MSE A 24 UNP P27431 EXPRESSION TAG SEQADV 4LIU THR A 25 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLY A 26 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLY A 27 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLU A 28 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLU A 29 UNP P27431 EXPRESSION TAG SEQADV 4LIU MSE A 30 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLY A 31 UNP P27431 EXPRESSION TAG SEQADV 4LIU ARG A 32 UNP P27431 EXPRESSION TAG SEQADV 4LIU GLY A 33 UNP P27431 EXPRESSION TAG SEQADV 4LIU SER A 34 UNP P27431 EXPRESSION TAG SEQADV 4LIU MSE A 35 UNP P27431 EXPRESSION TAG SEQRES 1 A 407 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 407 LEU VAL PRO ARG GLY SER HIS MSE ALA SER MSE THR GLY SEQRES 3 A 407 GLY GLU GLU MSE GLY ARG GLY SER MSE 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 MSE 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 MSE ARG PRO PHE ARG GLU LEU PRO ASP TRP ARG ILE ASP SEQRES 12 A 407 ASP LEU MSE 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 MSE 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 MSE 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 MSE ASP LYS LEU ARG GLU SEQRES 23 A 407 MSE MSE 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 MSE LEU ALA ALA LEU VAL ASN SER GLY TYR TRP SEQRES 32 A 407 PHE PHE GLU GLY MODRES 4LIU MSE A 35 MET SELENOMETHIONINE MODRES 4LIU MSE A 79 MET SELENOMETHIONINE MODRES 4LIU MSE A 131 MET SELENOMETHIONINE MODRES 4LIU MSE A 146 MET SELENOMETHIONINE MODRES 4LIU MSE A 230 MET SELENOMETHIONINE MODRES 4LIU MSE A 281 MET SELENOMETHIONINE MODRES 4LIU MSE A 287 MET SELENOMETHIONINE MODRES 4LIU MSE A 288 MET SELENOMETHIONINE MODRES 4LIU MSE A 393 MET SELENOMETHIONINE HET MSE A 35 8 HET MSE A 79 8 HET MSE A 131 8 HET MSE A 146 8 HET MSE A 230 8 HET MSE A 281 8 HET MSE A 287 8 HET MSE A 288 8 HET MSE A 393 8 HET TAM A 501 11 HET PO4 A 502 5 HETNAM MSE SELENOMETHIONINE HETNAM TAM TRIS(HYDROXYETHYL)AMINOMETHANE HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 2 TAM C7 H17 N O3 FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *113(H2 O) HELIX 1 1 ASN A 42 HIS A 50 1 9 HELIX 2 2 SER A 70 ALA A 78 1 9 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 ARG A 135 5 6 HELIX 6 6 ASN A 240 ARG A 255 1 16 HELIX 7 7 LEU A 277 ASN A 293 1 17 HELIX 8 8 GLN A 294 ILE A 306 1 13 HELIX 9 9 GLN A 323 GLN A 333 1 11 HELIX 10 10 HIS A 363 ASN A 373 1 11 HELIX 11 11 THR A 377 GLY A 382 1 6 HELIX 12 12 ASP A 383 GLU A 386 5 4 HELIX 13 13 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 VAL A 234 N PHE A 166 SHEET 5 A 8 ILE A 142 SER A 150 -1 N SER A 150 O ALA A 229 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 SER A 98 N LEU A 87 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 TYR A 353 N LEU A 346 SHEET 3 D 3 GLU A 357 ILE A 359 -1 O ILE A 359 N VAL A 352 LINK C MSE A 35 N GLU A 36 1555 1555 1.33 LINK C ALA A 78 N MSE A 79 1555 1555 1.33 LINK C MSE A 79 N GLU A 80 1555 1555 1.33 LINK C LEU A 130 N MSE A 131 1555 1555 1.33 LINK C MSE A 131 N ARG A 132 1555 1555 1.33 LINK C LEU A 145 N MSE A 146 1555 1555 1.33 LINK C MSE A 146 N ILE A 147 1555 1555 1.33 LINK C ALA A 229 N MSE A 230 1555 1555 1.33 LINK C MSE A 230 N ASN A 231 1555 1555 1.33 LINK C GLU A 280 N MSE A 281 1555 1555 1.33 LINK C MSE A 281 N ASP A 282 1555 1555 1.33 LINK C GLU A 286 N MSE A 287 1555 1555 1.33 LINK C MSE A 287 N MSE A 288 1555 1555 1.33 LINK C MSE A 288 N LEU A 289 1555 1555 1.33 LINK C ALA A 392 N MSE A 393 1555 1555 1.33 LINK C MSE A 393 N LEU A 394 1555 1555 1.33 CISPEP 1 GLY A 100 PRO A 101 0 2.23 CISPEP 2 GLU A 319 PRO A 320 0 2.31 SITE 1 AC1 5 LEU A 41 ASN A 42 ASP A 45 GLY A 407 SITE 2 AC1 5 HOH A 704 SITE 1 AC2 10 LEU A 116 MSE A 146 SER A 148 ARG A 174 SITE 2 AC2 10 TRP A 176 HOH A 607 HOH A 613 HOH A 671 SITE 3 AC2 10 HOH A 678 HOH A 708 CRYST1 75.110 75.110 209.950 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 0.013314 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004763 0.00000 HETATM 1 N MSE A 35 29.138 -18.813 29.448 1.00 97.16 N ANISOU 1 N MSE A 35 8918 14033 13964 2997 -164 -2611 N HETATM 2 CA MSE A 35 28.104 -18.481 30.423 1.00 93.45 C ANISOU 2 CA MSE A 35 8790 13550 13168 3042 -368 -2092 C HETATM 3 C MSE A 35 26.752 -18.238 29.757 1.00 84.37 C ANISOU 3 C MSE A 35 8148 12239 11670 2846 -14 -1895 C HETATM 4 O MSE A 35 26.518 -17.181 29.168 1.00 76.48 O ANISOU 4 O MSE A 35 7325 11458 10277 2474 443 -1982 O HETATM 5 CB MSE A 35 28.510 -17.253 31.242 1.00 95.26 C ANISOU 5 CB MSE A 35 8847 14311 13035 2838 -345 -2139 C HETATM 6 CG MSE A 35 27.511 -16.876 32.328 1.00 92.09 C ANISOU 6 CG MSE A 35 8749 14000 12242 2868 -556 -1630 C HETATM 7 SE MSE A 35 28.087 -15.356 33.410 1.00232.88 SE ANISOU 7 SE MSE A 35 26452 32486 29545 2346 -415 -1681 SE HETATM 8 CE MSE A 35 27.994 -13.946 32.064 1.00 51.91 C ANISOU 8 CE MSE A 35 3713 9708 6304 1834 612 -2134 C