HEADER OXIDOREDUCTASE 03-JUL-13 4LIV TITLE STRUCTURE OF YCFD, A RIBOSOMAL OXYGENASE FROM ESCHERICHIA COLI IN TITLE 2 COMPLEX WITH COBALT AND SUCCINIC ACID. 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 5 20-SEP-23 4LIV 1 REMARK REVDAT 4 20-NOV-19 4LIV 1 SEQADV LINK REVDAT 3 09-JUL-14 4LIV 1 JRNL REVDAT 2 25-JUN-14 4LIV 1 JRNL REVDAT 1 14-MAY-14 4LIV 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) : 53.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 30982 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1561 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 53.0503 - 6.0022 0.97 2635 120 0.1983 0.2364 REMARK 3 2 6.0022 - 4.7651 0.98 2644 152 0.1784 0.2322 REMARK 3 3 4.7651 - 4.1630 0.99 2675 109 0.1548 0.1656 REMARK 3 4 4.1630 - 3.7825 0.99 2686 137 0.1707 0.2598 REMARK 3 5 3.7825 - 3.5115 0.99 2660 157 0.1886 0.2756 REMARK 3 6 3.5115 - 3.3045 0.99 2699 132 0.1909 0.2723 REMARK 3 7 3.3045 - 3.1390 1.00 2675 153 0.2020 0.2284 REMARK 3 8 3.1390 - 3.0024 1.00 2671 132 0.2274 0.2370 REMARK 3 9 3.0024 - 2.8868 1.00 2706 144 0.2370 0.2508 REMARK 3 10 2.8868 - 2.7872 1.00 2670 164 0.2609 0.3573 REMARK 3 11 2.7872 - 2.7000 1.00 2700 161 0.2825 0.3517 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.33 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 2989 REMARK 3 ANGLE : 0.911 4072 REMARK 3 CHIRALITY : 0.070 415 REMARK 3 PLANARITY : 0.004 549 REMARK 3 DIHEDRAL : 15.913 1097 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 36:84) REMARK 3 ORIGIN FOR THE GROUP (A): 10.9227 -14.8277 -31.3276 REMARK 3 T TENSOR REMARK 3 T11: 0.2219 T22: 0.2056 REMARK 3 T33: 0.2194 T12: 0.0465 REMARK 3 T13: -0.0220 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 3.2656 L22: 2.9769 REMARK 3 L33: 3.6689 L12: 1.1487 REMARK 3 L13: 0.2231 L23: 0.1130 REMARK 3 S TENSOR REMARK 3 S11: -0.0756 S12: -0.0754 S13: -0.2335 REMARK 3 S21: -0.1758 S22: 0.0817 S23: -0.2837 REMARK 3 S31: 0.1435 S32: 0.2061 S33: 0.0077 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 85:104) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0009 -18.5340 -31.9169 REMARK 3 T TENSOR REMARK 3 T11: 0.2572 T22: 0.7021 REMARK 3 T33: 0.4530 T12: -0.0671 REMARK 3 T13: 0.0213 T23: 0.0793 REMARK 3 L TENSOR REMARK 3 L11: 3.3519 L22: 8.3096 REMARK 3 L33: 6.9109 L12: 0.2686 REMARK 3 L13: -1.2601 L23: -1.8294 REMARK 3 S TENSOR REMARK 3 S11: 0.5457 S12: -0.1004 S13: -0.7134 REMARK 3 S21: 0.0934 S22: 0.2005 S23: 1.2041 REMARK 3 S31: 0.0081 S32: -1.3255 S33: -0.6117 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 105:140) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9364 -20.4328 -27.5514 REMARK 3 T TENSOR REMARK 3 T11: 0.2505 T22: 0.2513 REMARK 3 T33: 0.2843 T12: 0.0124 REMARK 3 T13: -0.0028 T23: -0.0187 REMARK 3 L TENSOR REMARK 3 L11: 1.1463 L22: 2.3385 REMARK 3 L33: 3.2441 L12: -0.0330 REMARK 3 L13: 0.6727 L23: -0.4770 REMARK 3 S TENSOR REMARK 3 S11: 0.1810 S12: 0.0023 S13: -0.4252 REMARK 3 S21: -0.0156 S22: 0.1526 S23: -0.1069 REMARK 3 S31: 0.3488 S32: -0.2229 S33: -0.3589 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 141:234) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0720 -9.2910 -34.6950 REMARK 3 T TENSOR REMARK 3 T11: 0.2267 T22: 0.2977 REMARK 3 T33: 0.2190 T12: 0.0213 REMARK 3 T13: 0.0007 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 2.4115 L22: 2.0094 REMARK 3 L33: 2.9166 L12: 0.8244 REMARK 3 L13: 0.8245 L23: -0.7917 REMARK 3 S TENSOR REMARK 3 S11: -0.1306 S12: 0.1311 S13: 0.0958 REMARK 3 S21: -0.1725 S22: 0.2017 S23: 0.1262 REMARK 3 S31: -0.1372 S32: -0.3120 S33: -0.0858 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 235:273) REMARK 3 ORIGIN FOR THE GROUP (A): 0.2266 1.4773 4.2994 REMARK 3 T TENSOR REMARK 3 T11: 0.3271 T22: 0.3514 REMARK 3 T33: 0.3886 T12: 0.0634 REMARK 3 T13: -0.0166 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 1.0647 L22: 1.7268 REMARK 3 L33: 4.8468 L12: -0.8040 REMARK 3 L13: -1.8530 L23: 2.7533 REMARK 3 S TENSOR REMARK 3 S11: 0.0061 S12: 0.0311 S13: -0.1113 REMARK 3 S21: 0.0341 S22: -0.1160 S23: 0.2851 REMARK 3 S31: 0.1232 S32: -0.1170 S33: 0.1046 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 274:293) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1764 10.9701 7.3506 REMARK 3 T TENSOR REMARK 3 T11: 0.3930 T22: 0.4855 REMARK 3 T33: 0.3268 T12: -0.0346 REMARK 3 T13: 0.0433 T23: 0.0395 REMARK 3 L TENSOR REMARK 3 L11: 2.9863 L22: 5.6469 REMARK 3 L33: 3.5522 L12: -3.7807 REMARK 3 L13: -3.0528 L23: 4.4744 REMARK 3 S TENSOR REMARK 3 S11: 0.2157 S12: 0.3853 S13: 0.2008 REMARK 3 S21: -0.1109 S22: 0.1188 S23: -0.5541 REMARK 3 S31: -0.2561 S32: 0.0847 S33: -0.3646 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 294:312) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7043 -10.5368 -4.6933 REMARK 3 T TENSOR REMARK 3 T11: 0.6006 T22: 0.5187 REMARK 3 T33: 0.4628 T12: 0.2433 REMARK 3 T13: 0.0277 T23: 0.0540 REMARK 3 L TENSOR REMARK 3 L11: 3.3354 L22: 5.0092 REMARK 3 L33: 8.6575 L12: 1.5631 REMARK 3 L13: 1.5780 L23: 5.5852 REMARK 3 S TENSOR REMARK 3 S11: 0.2062 S12: -0.5263 S13: 0.2127 REMARK 3 S21: 0.1586 S22: 0.1695 S23: -0.2704 REMARK 3 S31: -0.5449 S32: -0.7284 S33: -0.3337 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 313:350) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5597 -30.0571 -8.0738 REMARK 3 T TENSOR REMARK 3 T11: 0.3374 T22: 0.2952 REMARK 3 T33: 0.2898 T12: 0.0161 REMARK 3 T13: -0.0212 T23: 0.0732 REMARK 3 L TENSOR REMARK 3 L11: 3.0055 L22: 2.2545 REMARK 3 L33: 1.7900 L12: -2.5767 REMARK 3 L13: 0.2416 L23: -0.4985 REMARK 3 S TENSOR REMARK 3 S11: -0.0972 S12: -0.2259 S13: -0.2224 REMARK 3 S21: -0.2483 S22: 0.2471 S23: 0.1495 REMARK 3 S31: 0.1167 S32: -0.1028 S33: -0.1337 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 351:378) REMARK 3 ORIGIN FOR THE GROUP (A): 19.5805 -20.2914 -5.9798 REMARK 3 T TENSOR REMARK 3 T11: 0.4014 T22: 0.3516 REMARK 3 T33: 0.3895 T12: -0.0411 REMARK 3 T13: -0.0528 T23: 0.0321 REMARK 3 L TENSOR REMARK 3 L11: 3.7620 L22: 5.1740 REMARK 3 L33: 2.8080 L12: -3.7393 REMARK 3 L13: -0.2689 L23: -0.1280 REMARK 3 S TENSOR REMARK 3 S11: -0.1474 S12: -0.3062 S13: 0.4717 REMARK 3 S21: 0.4480 S22: 0.0098 S23: -0.6732 REMARK 3 S31: -0.3159 S32: 0.0981 S33: 0.0829 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 379:407) REMARK 3 ORIGIN FOR THE GROUP (A): 19.3228 -29.5954 -5.3440 REMARK 3 T TENSOR REMARK 3 T11: 0.4045 T22: 0.3409 REMARK 3 T33: 0.3666 T12: 0.0495 REMARK 3 T13: 0.0056 T23: 0.0535 REMARK 3 L TENSOR REMARK 3 L11: 1.8654 L22: 1.0473 REMARK 3 L33: 1.2128 L12: -0.0288 REMARK 3 L13: 0.1176 L23: -0.2854 REMARK 3 S TENSOR REMARK 3 S11: 0.1149 S12: -0.0495 S13: -0.1428 REMARK 3 S21: -0.1038 S22: 0.1090 S23: 0.0179 REMARK 3 S31: 0.0281 S32: -0.1358 S33: -0.1566 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 4LIV 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_1000080684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16951 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 70.601 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.17900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.89500 REMARK 200 R SYM FOR SHELL (I) : 0.89500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900 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 (%): 61.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM COBALT CHLORIDE, 50MM SUCCINIC REMARK 280 ACID PH 4.2, 1.2M 1,6 HEXANEDIOL., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 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 104.50000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.50500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 156.75000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.50500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.50500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.25000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.50500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.50500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 156.75000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.50500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.50500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.25000 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 104.50000 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: 6790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 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 465 LEU A 194 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 LYS A 94 CG CD CE NZ REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 ASP A 106 CG OD1 OD2 REMARK 470 GLN A 195 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 640 O HOH A 651 1.93 REMARK 500 O HOH A 676 O HOH A 713 1.95 REMARK 500 O HOH A 697 O HOH A 718 2.02 REMARK 500 O HOH A 619 O HOH A 624 2.03 REMARK 500 O GLU A 200 O HOH A 709 2.06 REMARK 500 N GLN A 195 O HOH A 714 2.07 REMARK 500 O HOH A 703 O HOH A 705 2.08 REMARK 500 NH2 ARG A 141 O HOH A 707 2.11 REMARK 500 OD2 ASP A 360 O HOH A 724 2.15 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 -52.52 -135.95 REMARK 500 ASP A 143 -108.50 -103.46 REMARK 500 ASP A 266 48.55 -100.59 REMARK 500 GLU A 406 -57.98 70.67 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 87.9 REMARK 620 3 HIS A 221 NE2 77.5 87.4 REMARK 620 4 SIN A 502 O2 108.2 163.3 100.1 REMARK 620 5 SIN A 502 O1 98.2 119.9 152.4 54.9 REMARK 620 N 1 2 3 4 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 SIN 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: 4LIU RELATED DB: PDB REMARK 900 SAME PROTEIN - APO FORM DBREF 4LIV A 35 407 UNP P27431 YCFD_ECOLI 1 373 SEQADV 4LIV MET A 1 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLY A 2 UNP P27431 EXPRESSION TAG SEQADV 4LIV SER A 3 UNP P27431 EXPRESSION TAG SEQADV 4LIV SER A 4 UNP P27431 EXPRESSION TAG SEQADV 4LIV HIS A 5 UNP P27431 EXPRESSION TAG SEQADV 4LIV HIS A 6 UNP P27431 EXPRESSION TAG SEQADV 4LIV HIS A 7 UNP P27431 EXPRESSION TAG SEQADV 4LIV HIS A 8 UNP P27431 EXPRESSION TAG SEQADV 4LIV HIS A 9 UNP P27431 EXPRESSION TAG SEQADV 4LIV HIS A 10 UNP P27431 EXPRESSION TAG SEQADV 4LIV SER A 11 UNP P27431 EXPRESSION TAG SEQADV 4LIV SER A 12 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLY A 13 UNP P27431 EXPRESSION TAG SEQADV 4LIV LEU A 14 UNP P27431 EXPRESSION TAG SEQADV 4LIV VAL A 15 UNP P27431 EXPRESSION TAG SEQADV 4LIV PRO A 16 UNP P27431 EXPRESSION TAG SEQADV 4LIV ARG A 17 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLY A 18 UNP P27431 EXPRESSION TAG SEQADV 4LIV SER A 19 UNP P27431 EXPRESSION TAG SEQADV 4LIV HIS A 20 UNP P27431 EXPRESSION TAG SEQADV 4LIV MET A 21 UNP P27431 EXPRESSION TAG SEQADV 4LIV ALA A 22 UNP P27431 EXPRESSION TAG SEQADV 4LIV SER A 23 UNP P27431 EXPRESSION TAG SEQADV 4LIV MET A 24 UNP P27431 EXPRESSION TAG SEQADV 4LIV THR A 25 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLY A 26 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLY A 27 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLU A 28 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLU A 29 UNP P27431 EXPRESSION TAG SEQADV 4LIV MET A 30 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLY A 31 UNP P27431 EXPRESSION TAG SEQADV 4LIV ARG A 32 UNP P27431 EXPRESSION TAG SEQADV 4LIV GLY A 33 UNP P27431 EXPRESSION TAG SEQADV 4LIV 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 SIN A 502 8 HETNAM CO COBALT (II) ION HETNAM SIN SUCCINIC ACID FORMUL 2 CO CO 2+ FORMUL 3 SIN C4 H6 O4 FORMUL 4 HOH *124(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 ASN A 240 ARG A 255 1 16 HELIX 7 7 LEU A 277 GLN A 294 1 18 HELIX 8 8 GLU A 296 SER A 307 1 12 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 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 SER A 98 N LEU A 87 SHEET 1 B 3 ALA A 201 LEU A 207 0 SHEET 2 B 3 ARG A 174 GLY A 179 -1 N TRP A 176 O GLU A 205 SHEET 3 B 3 HIS A 221 ALA A 225 -1 O TYR A 224 N ARG A 175 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 NE2 HIS A 159 CO CO A 501 1555 1555 2.04 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 O2 SIN A 502 1555 1555 2.29 LINK CO CO A 501 O1 SIN A 502 1555 1555 2.38 CISPEP 1 GLY A 100 PRO A 101 0 0.82 CISPEP 2 GLU A 319 PRO A 320 0 1.82 SITE 1 AC1 4 HIS A 159 ASP A 161 HIS A 221 SIN A 502 SITE 1 AC2 10 MET A 146 SER A 148 HIS A 159 ARG A 174 SITE 2 AC2 10 TRP A 176 HIS A 221 ASN A 231 CO A 501 SITE 3 AC2 10 HOH A 603 HOH A 609 CRYST1 75.010 75.010 209.000 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 0.013332 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004785 0.00000