HEADER OXIDOREDUCTASE/RNA 20-FEB-15 4YCP TITLE E. COLI DIHYDROURIDINE SYNTHASE C (DUSC) IN COMPLEX WITH TRNATRP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA-DIHYDROURIDINE SYNTHASE C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-315; COMPND 5 SYNONYM: DUSC; COMPND 6 EC: 1.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TRNATRP; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: DUSC, YOHI, B2140, JW2128; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 12 ORGANISM_TAXID: 83333 KEYWDS TRNA MODIFICATION, OXIDOREDUCTASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.T.BYRNE,H.T.JENKINS,D.T.PETERS,F.WHELAN,J.STOWELL,N.AZIZ, AUTHOR 2 P.KASATSKY,M.V.RODNINA,E.V.KOONIN,A.L.KONEVEGA,A.A.ANTSON REVDAT 4 10-JAN-24 4YCP 1 LINK REVDAT 3 20-MAY-15 4YCP 1 JRNL REVDAT 2 13-MAY-15 4YCP 1 JRNL REVDAT 1 22-APR-15 4YCP 0 JRNL AUTH R.T.BYRNE,H.T.JENKINS,D.T.PETERS,F.WHELAN,J.STOWELL,N.AZIZ, JRNL AUTH 2 P.KASATSKY,M.V.RODNINA,E.V.KOONIN,A.L.KONEVEGA,A.A.ANTSON JRNL TITL MAJOR REORIENTATION OF TRNA SUBSTRATES DEFINES SPECIFICITY JRNL TITL 2 OF DIHYDROURIDINE SYNTHASES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 6033 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 25902496 JRNL DOI 10.1073/PNAS.1500161112 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 21202 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1534 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2398 REMARK 3 NUCLEIC ACID ATOMS : 1287 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 1.70000 REMARK 3 B12 (A**2) : -0.26000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.427 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.258 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.218 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.303 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3926 ; 0.006 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): 2974 ; 0.002 ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5621 ; 1.003 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): 6884 ; 1.044 ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 321 ; 5.578 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;37.222 ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 409 ;12.994 ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.998 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 620 ; 0.061 ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3624 ; 0.004 ; NULL REMARK 3 GENERAL PLANES OTHERS (A): 884 ; 0.001 ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1230 ; 0.318 ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1229 ; 0.318 ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1534 ; 0.562 ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 45 REMARK 3 ORIGIN FOR THE GROUP (A): 27.7179 -42.2182 -4.3455 REMARK 3 T TENSOR REMARK 3 T11: 0.0720 T22: 0.1980 REMARK 3 T33: 0.0063 T12: -0.0670 REMARK 3 T13: 0.0037 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 2.1395 L22: 2.8411 REMARK 3 L33: 2.9630 L12: -0.3908 REMARK 3 L13: 0.4031 L23: 0.4774 REMARK 3 S TENSOR REMARK 3 S11: -0.0587 S12: -0.2361 S13: 0.0300 REMARK 3 S21: -0.0443 S22: 0.0155 S23: -0.1115 REMARK 3 S31: 0.2076 S32: -0.2014 S33: 0.0432 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 46 A 163 REMARK 3 ORIGIN FOR THE GROUP (A): 36.3254 -50.7130 -7.3043 REMARK 3 T TENSOR REMARK 3 T11: 0.1714 T22: 0.2080 REMARK 3 T33: 0.0404 T12: -0.0239 REMARK 3 T13: 0.0075 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.9897 L22: 2.1101 REMARK 3 L33: 3.2542 L12: -0.1589 REMARK 3 L13: 0.1925 L23: 0.6564 REMARK 3 S TENSOR REMARK 3 S11: -0.0419 S12: -0.2047 S13: -0.2209 REMARK 3 S21: 0.1512 S22: 0.0872 S23: -0.1157 REMARK 3 S31: 0.6297 S32: 0.2348 S33: -0.0453 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 164 A 257 REMARK 3 ORIGIN FOR THE GROUP (A): 39.2024 -32.1907 -0.5191 REMARK 3 T TENSOR REMARK 3 T11: 0.1054 T22: 0.2355 REMARK 3 T33: 0.1270 T12: -0.0840 REMARK 3 T13: -0.0628 T23: -0.0346 REMARK 3 L TENSOR REMARK 3 L11: 3.4707 L22: 2.0612 REMARK 3 L33: 2.6492 L12: -1.4060 REMARK 3 L13: -0.9049 L23: 0.5217 REMARK 3 S TENSOR REMARK 3 S11: -0.0985 S12: -0.1896 S13: 0.2570 REMARK 3 S21: 0.0854 S22: 0.1658 S23: -0.3367 REMARK 3 S31: -0.3028 S32: 0.2638 S33: -0.0673 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 258 A 315 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7742 -30.4133 10.2686 REMARK 3 T TENSOR REMARK 3 T11: 0.2505 T22: 0.4130 REMARK 3 T33: 0.0578 T12: 0.1366 REMARK 3 T13: 0.0127 T23: -0.0504 REMARK 3 L TENSOR REMARK 3 L11: 3.8270 L22: 6.0735 REMARK 3 L33: 2.5255 L12: 1.1705 REMARK 3 L13: -1.2771 L23: -1.1612 REMARK 3 S TENSOR REMARK 3 S11: -0.0031 S12: -0.1765 S13: 0.4285 REMARK 3 S21: 0.5097 S22: 0.1320 S23: 0.2966 REMARK 3 S31: -0.6593 S32: -0.6190 S33: -0.1290 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 5 B 21 REMARK 3 ORIGIN FOR THE GROUP (A): 25.1050 -55.8330 12.3847 REMARK 3 T TENSOR REMARK 3 T11: 0.3030 T22: 0.3562 REMARK 3 T33: 0.1826 T12: -0.1055 REMARK 3 T13: -0.0034 T23: 0.0792 REMARK 3 L TENSOR REMARK 3 L11: 0.1726 L22: 6.4701 REMARK 3 L33: 0.5126 L12: 0.7768 REMARK 3 L13: -0.0523 L23: 0.9557 REMARK 3 S TENSOR REMARK 3 S11: -0.0349 S12: -0.1110 S13: -0.1237 REMARK 3 S21: 0.2132 S22: -0.1120 S23: -0.2944 REMARK 3 S31: 0.2181 S32: 0.1214 S33: 0.1470 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 22 B 32 REMARK 3 ORIGIN FOR THE GROUP (A): 9.6601 -66.0161 -1.4130 REMARK 3 T TENSOR REMARK 3 T11: 0.4459 T22: 0.4717 REMARK 3 T33: 0.3124 T12: -0.0740 REMARK 3 T13: -0.1159 T23: -0.0441 REMARK 3 L TENSOR REMARK 3 L11: 5.3225 L22: 3.4264 REMARK 3 L33: 1.0507 L12: -0.4140 REMARK 3 L13: 0.0906 L23: 1.0658 REMARK 3 S TENSOR REMARK 3 S11: 0.0779 S12: 0.6801 S13: -0.1106 REMARK 3 S21: -0.3552 S22: -0.3402 S23: 0.8822 REMARK 3 S31: -0.1247 S32: -0.4528 S33: 0.2623 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 36 B 42 REMARK 3 ORIGIN FOR THE GROUP (A): 6.7879 -70.9474 -8.5474 REMARK 3 T TENSOR REMARK 3 T11: 0.6845 T22: 0.5973 REMARK 3 T33: 0.6283 T12: -0.0112 REMARK 3 T13: -0.1051 T23: -0.1685 REMARK 3 L TENSOR REMARK 3 L11: 3.1931 L22: 3.7268 REMARK 3 L33: 1.9877 L12: -2.7799 REMARK 3 L13: -0.7361 L23: 2.1796 REMARK 3 S TENSOR REMARK 3 S11: -0.0839 S12: 0.2389 S13: 0.4833 REMARK 3 S21: -0.2745 S22: -0.1342 S23: -0.1829 REMARK 3 S31: -0.4161 S32: 0.0016 S33: 0.2182 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 43 B 47 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8122 -58.8188 5.8729 REMARK 3 T TENSOR REMARK 3 T11: 0.6315 T22: 0.4893 REMARK 3 T33: 0.5138 T12: 0.0529 REMARK 3 T13: -0.0375 T23: -0.1287 REMARK 3 L TENSOR REMARK 3 L11: 17.5246 L22: 0.6361 REMARK 3 L33: 15.7174 L12: 3.3033 REMARK 3 L13: 16.5753 L23: 3.1038 REMARK 3 S TENSOR REMARK 3 S11: -0.5703 S12: -1.0867 S13: 0.8746 REMARK 3 S21: -0.0231 S22: -0.2277 S23: 0.1784 REMARK 3 S31: -0.6897 S32: -1.0478 S33: 0.7980 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 48 B 69 REMARK 3 ORIGIN FOR THE GROUP (A): 25.4969 -52.5943 25.1533 REMARK 3 T TENSOR REMARK 3 T11: 0.4918 T22: 0.3552 REMARK 3 T33: 0.1325 T12: -0.0448 REMARK 3 T13: 0.0185 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 0.3160 L22: 5.4445 REMARK 3 L33: 3.4862 L12: 0.9911 REMARK 3 L13: -0.3637 L23: -3.6159 REMARK 3 S TENSOR REMARK 3 S11: 0.0593 S12: -0.0733 S13: -0.1552 REMARK 3 S21: 0.5085 S22: -0.1136 S23: -0.3331 REMARK 3 S31: 0.0297 S32: -0.0445 S33: 0.0542 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4YCP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96861 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22329 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 49.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 1.09900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4BFA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 0.2 M LI2SO4 REMARK 280 26% PEG 2K MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 154.11467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.05733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 115.58600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 38.52867 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 192.64333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 154.11467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 77.05733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 38.52867 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 115.58600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 192.64333 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: 3680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 508 LIES ON A SPECIAL POSITION. 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 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 SER A 100 REMARK 465 LYS A 101 REMARK 465 THR A 102 REMARK 465 VAL A 103 REMARK 465 ASN A 104 REMARK 465 GLY A 105 REMARK 465 SER A 106 REMARK 465 A B 1 REMARK 465 G B 2 REMARK 465 G B 3 REMARK 465 G B 4 REMARK 465 U B 33 REMARK 465 C B 34 REMARK 465 C B 35 REMARK 465 C B 70 REMARK 465 C B 71 REMARK 465 U B 72 REMARK 465 G B 73 REMARK 465 C B 74 REMARK 465 C B 75 REMARK 465 A B 76 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 149 CG CD CE NZ REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 GLN A 211 CG CD OE1 NE2 REMARK 470 ASP A 311 CG OD1 OD2 REMARK 470 ILE A 312 CG1 CG2 CD1 REMARK 470 GLU A 313 CG CD OE1 OE2 REMARK 470 LYS A 314 CG CD CE NZ REMARK 470 LEU A 315 CG CD1 CD2 REMARK 470 A B 36 P OP1 OP2 REMARK 470 U B 45 C5' C4' O4' C3' C2' O2' C1' REMARK 470 U B 45 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U B 45 C6 REMARK 470 U B 47 P OP1 OP2 O5' C5' C4' O4' REMARK 470 U B 47 C3' C2' O2' C1' N1 C2 O2 REMARK 470 U B 47 N3 C4 O4 C5 C6 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 VAL A 11 -64.94 -132.80 REMARK 500 VAL A 37 -90.77 -121.47 REMARK 500 TRP A 144 -72.43 -79.27 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 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 542 O REMARK 620 2 HOH A 543 O 82.2 REMARK 620 3 U B 17 OP2 168.6 94.9 REMARK 620 4 G B 19 OP2 100.4 101.7 91.0 REMARK 620 5 HOH B 207 O 81.1 80.1 87.6 177.8 REMARK 620 6 HOH B 208 O 88.5 163.2 91.5 93.6 84.8 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 FMN 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 MG B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YCO RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN COMPLEXED WITH TRNAPHE REMARK 900 RELATED ID: 4BFA RELATED DB: PDB REMARK 900 4BFA CONTAINS WILD-TYPE PROTEIN IN THE ABSENCE OF RNA. REMARK 900 RELATED ID: 4BF9 RELATED DB: PDB REMARK 900 4BFA CONTAINS WILD-TYPE PROTEIN IN THE ABSENCE OF RNA. DBREF 4YCP A 1 315 UNP P33371 DUSC_ECOLI 1 315 DBREF1 4YCP B 1 76 GB CP009789.1 DBREF2 4YCP B 731469900 3918611 3918686 SEQADV 4YCP GLY A -5 UNP P33371 EXPRESSION TAG SEQADV 4YCP SER A -4 UNP P33371 EXPRESSION TAG SEQADV 4YCP HIS A -3 UNP P33371 EXPRESSION TAG SEQADV 4YCP MET A -2 UNP P33371 EXPRESSION TAG SEQADV 4YCP ALA A -1 UNP P33371 EXPRESSION TAG SEQADV 4YCP SER A 0 UNP P33371 EXPRESSION TAG SEQADV 4YCP ALA A 98 UNP P33371 CYS 98 ENGINEERED MUTATION SEQRES 1 A 321 GLY SER HIS MET ALA SER MET ARG VAL LEU LEU ALA PRO SEQRES 2 A 321 MET GLU GLY VAL LEU ASP SER LEU VAL ARG GLU LEU LEU SEQRES 3 A 321 THR GLU VAL ASN ASP TYR ASP LEU CYS ILE THR GLU PHE SEQRES 4 A 321 VAL ARG VAL VAL ASP GLN LEU LEU PRO VAL LYS VAL PHE SEQRES 5 A 321 HIS ARG ILE CYS PRO GLU LEU GLN ASN ALA SER ARG THR SEQRES 6 A 321 PRO SER GLY THR LEU VAL ARG VAL GLN LEU LEU GLY GLN SEQRES 7 A 321 PHE PRO GLN TRP LEU ALA GLU ASN ALA ALA ARG ALA VAL SEQRES 8 A 321 GLU LEU GLY SER TRP GLY VAL ASP LEU ASN CYS GLY ALA SEQRES 9 A 321 PRO SER LYS THR VAL ASN GLY SER GLY GLY GLY ALA THR SEQRES 10 A 321 LEU LEU LYS ASP PRO GLU LEU ILE TYR GLN GLY ALA LYS SEQRES 11 A 321 ALA MET ARG GLU ALA VAL PRO ALA HIS LEU PRO VAL SER SEQRES 12 A 321 VAL LYS VAL ARG LEU GLY TRP ASP SER GLY GLU LYS LYS SEQRES 13 A 321 PHE GLU ILE ALA ASP ALA VAL GLN GLN ALA GLY ALA THR SEQRES 14 A 321 GLU LEU VAL VAL HIS GLY ARG THR LYS GLU GLN GLY TYR SEQRES 15 A 321 ARG ALA GLU HIS ILE ASP TRP GLN ALA ILE GLY ASP ILE SEQRES 16 A 321 ARG GLN ARG LEU ASN ILE PRO VAL ILE ALA ASN GLY GLU SEQRES 17 A 321 ILE TRP ASP TRP GLN SER ALA GLN GLN CYS MET ALA ILE SEQRES 18 A 321 SER GLY CYS ASP ALA VAL MET ILE GLY ARG GLY ALA LEU SEQRES 19 A 321 ASN ILE PRO ASN LEU SER ARG VAL VAL LYS TYR ASN GLU SEQRES 20 A 321 PRO ARG MET PRO TRP PRO GLU VAL VAL ALA LEU LEU GLN SEQRES 21 A 321 LYS TYR THR ARG LEU GLU LYS GLN GLY ASP THR GLY LEU SEQRES 22 A 321 TYR HIS VAL ALA ARG ILE LYS GLN TRP LEU SER TYR LEU SEQRES 23 A 321 ARG LYS GLU TYR ASP GLU ALA THR GLU LEU PHE GLN HIS SEQRES 24 A 321 VAL ARG VAL LEU ASN ASN SER PRO ASP ILE ALA ARG ALA SEQRES 25 A 321 ILE GLN ALA ILE ASP ILE GLU LYS LEU SEQRES 1 B 76 A G G G G C G U A G U U C SEQRES 2 B 76 A A U U G G U A G A G C A SEQRES 3 B 76 C C G G U C U C C A A A A SEQRES 4 B 76 C C G G G U G U U G G G A SEQRES 5 B 76 G U U C G A G U C U C U C SEQRES 6 B 76 C G C C C C U G C C A HET FMN A 401 31 HET SO4 A 402 5 HET SO4 A 403 5 HET MG B 101 1 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN C17 H21 N4 O9 P FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 MG MG 2+ FORMUL 7 HOH *52(H2 O) HELIX 1 AA1 ASP A 13 VAL A 23 1 11 HELIX 2 AA2 PRO A 42 CYS A 50 1 9 HELIX 3 AA3 PRO A 51 ALA A 56 5 6 HELIX 4 AA4 PHE A 73 LEU A 87 1 15 HELIX 5 AA5 GLY A 108 LYS A 114 5 7 HELIX 6 AA6 ASP A 115 VAL A 130 1 16 HELIX 7 AA7 LYS A 149 GLY A 161 1 13 HELIX 8 AA8 ARG A 177 ILE A 181 5 5 HELIX 9 AA9 ASP A 182 LEU A 193 1 12 HELIX 10 AB1 ASP A 205 GLY A 217 1 13 HELIX 11 AB2 ARG A 225 ILE A 230 1 6 HELIX 12 AB3 ASN A 232 ASN A 240 1 9 HELIX 13 AB4 PRO A 245 LEU A 259 1 15 HELIX 14 AB5 LEU A 267 ARG A 281 1 15 HELIX 15 AB6 LYS A 282 TYR A 284 5 3 HELIX 16 AB7 ASP A 285 ARG A 295 1 11 HELIX 17 AB8 ASN A 299 ALA A 309 1 11 HELIX 18 AB9 ASP A 311 LEU A 315 5 5 SHEET 1 AA110 VAL A 34 ARG A 35 0 SHEET 2 AA110 VAL A 65 LEU A 70 1 O GLN A 68 N VAL A 34 SHEET 3 AA110 VAL A 92 CYS A 96 1 O ASP A 93 N LEU A 69 SHEET 4 AA110 VAL A 136 ARG A 141 1 O LYS A 139 N LEU A 94 SHEET 5 AA110 GLU A 164 HIS A 168 1 O VAL A 166 N VAL A 138 SHEET 6 AA110 VAL A 197 ASN A 200 1 O ILE A 198 N LEU A 165 SHEET 7 AA110 ALA A 220 ILE A 223 1 O MET A 222 N ALA A 199 SHEET 8 AA110 ARG A 2 LEU A 5 1 N LEU A 4 O VAL A 221 SHEET 9 AA110 LEU A 28 ILE A 30 1 O LEU A 28 N LEU A 5 SHEET 10 AA110 VAL A 65 LEU A 70 1 O ARG A 66 N CYS A 29 LINK O HOH A 542 MG MG B 101 1555 1555 2.18 LINK O HOH A 543 MG MG B 101 1555 1555 2.19 LINK OP2 U B 17 MG MG B 101 1555 1555 2.03 LINK OP2 G B 19 MG MG B 101 1555 1555 2.01 LINK MG MG B 101 O HOH B 207 1555 1555 2.18 LINK MG MG B 101 O HOH B 208 1555 1555 2.18 SITE 1 AC1 19 ALA A 6 PRO A 7 MET A 8 GLU A 9 SITE 2 AC1 19 PHE A 33 GLN A 68 ASN A 95 LYS A 139 SITE 3 AC1 19 HIS A 168 TYR A 176 ASN A 200 GLY A 201 SITE 4 AC1 19 GLU A 202 GLY A 224 ARG A 225 HOH A 540 SITE 5 AC1 19 HOH A 541 U B 16 U B 17 SITE 1 AC2 3 ARG A 281 PHE A 291 ARG A 295 SITE 1 AC3 3 ARG A 243 PRO A 245 TRP A 246 SITE 1 AC4 6 HOH A 542 HOH A 543 U B 17 G B 19 SITE 2 AC4 6 HOH B 207 HOH B 208 CRYST1 98.516 98.516 231.172 90.00 90.00 120.00 P 65 2 2 12 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 0.010151 0.005860 0.000000 0.00000 SCALE2 0.000000 0.011721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004326 0.00000