HEADER OXIDOREDUCTASE 16-MAR-13 4BF9 TITLE CRYSTAL STRUCTURE OF E. COLI DIHYDROURIDINE SYNTHASE C (DUSC) TITLE 2 (SELENOMETHIONINE DERIVATIVE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA-DIHYDROURIDINE SYNTHASE C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIHYDROURIDINE SYNTHASE C; COMPND 5 EC: 1.3.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: MG1655; SOURCE 5 ATCC: 700926; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS TRNA MODIFICATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION MDLTYP P ATOMS ONLY, CHAIN B AUTHOR R.T.BYRNE,F.WHELAN,A.KONEVEGA,N.AZIZ,M.RODNINA,A.A.ANTSON REVDAT 4 27-MAY-15 4BF9 1 JRNL REVDAT 3 13-MAY-15 4BF9 1 JRNL REVDAT 2 22-APR-15 4BF9 1 JRNL REVDAT 1 06-NOV-13 4BF9 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 ISSN 0027-8424 JRNL PMID 25902496 JRNL DOI 10.1073/PNAS.1500161112 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.64 REMARK 3 NUMBER OF REFLECTIONS : 16226 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) : 0.17858 REMARK 3 R VALUE (WORKING SET) : 0.17668 REMARK 3 FREE R VALUE : 0.21447 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 860 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) : 2.600 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.667 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1175 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.280 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.277 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2495 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.164 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.91 REMARK 3 B22 (A**2) : 0.91 REMARK 3 B33 (A**2) : -1.82 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.318 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.229 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.027 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2577 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2500 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3505 ; 1.431 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5730 ; 0.777 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 317 ; 6.274 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;37.194 ;24.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 421 ;14.521 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;19.832 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 391 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3013 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 580 ; 0.001 ; 0.020 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): 1271 ; 1.456 ; 2.957 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1270 ; 1.456 ; 2.956 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1587 ; 2.308 ; 4.431 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1306 ; 1.883 ; 3.160 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1919 ; 3.067 ; 4.658 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 : 2 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 -2 A 228 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3862 31.1483 50.6883 REMARK 3 T TENSOR REMARK 3 T11: 0.0400 T22: 0.0228 REMARK 3 T33: 0.0491 T12: 0.0128 REMARK 3 T13: -0.0327 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 3.0112 L22: 3.0643 REMARK 3 L33: 1.8682 L12: 0.4093 REMARK 3 L13: -1.4270 L23: -0.5116 REMARK 3 S TENSOR REMARK 3 S11: 0.0532 S12: 0.1903 S13: 0.1192 REMARK 3 S21: -0.1864 S22: -0.0054 S23: 0.1972 REMARK 3 S31: -0.1228 S32: -0.1865 S33: -0.0478 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 229 A 315 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0502 52.6344 60.7238 REMARK 3 T TENSOR REMARK 3 T11: 0.4809 T22: 0.1866 REMARK 3 T33: 0.3886 T12: 0.1393 REMARK 3 T13: 0.1428 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 3.2849 L22: 8.3275 REMARK 3 L33: 8.7067 L12: 0.7257 REMARK 3 L13: 1.0150 L23: -4.0238 REMARK 3 S TENSOR REMARK 3 S11: -0.0311 S12: 0.2774 S13: 0.8186 REMARK 3 S21: -0.0844 S22: 0.2643 S23: 0.6487 REMARK 3 S31: -1.5297 S32: -0.7064 S33: -0.2333 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 REMARK 3 RIDING POSITIONS. U VALUES WITH TLS ADDED. REMARK 4 REMARK 4 4BF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-13. REMARK 100 THE PDBE ID CODE IS EBI-56168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-10 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 : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9808 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17124 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.60 REMARK 200 RESOLUTION RANGE LOW (A) : 59.80 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.7 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.20 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.9 REMARK 200 R MERGE FOR SHELL (I) : 0.843 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD, PHASER, PARROT, BUCCANEER REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.8 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOLECULAR DIMENSIONS MORPHEUS REMARK 280 SCREEN CONDITION D3 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 59.84000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.07000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.76000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.07000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.07000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.92000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.07000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.07000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 89.76000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.07000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.07000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.92000 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 59.84000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 VAL A -8 REMARK 465 PRO A -7 REMARK 465 ARG A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 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 -55.78 -128.85 REMARK 500 ASP A 25 59.49 -116.47 REMARK 500 LEU A 28 135.87 -174.67 REMARK 500 VAL A 37 -92.10 -113.40 REMARK 500 SER A 57 33.83 70.50 REMARK 500 TRP A 144 -70.03 -80.05 REMARK 500 LYS A 314 58.84 -67.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. 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 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BFA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI DIHYDROURIDINE SYNTHASE C REMARK 900 (DUSC) DBREF 4BF9 A 1 315 UNP P33371 DUSC_ECOLI 1 315 SEQADV 4BF9 MSE A -22 UNP P33371 EXPRESSION TAG SEQADV 4BF9 GLY A -21 UNP P33371 EXPRESSION TAG SEQADV 4BF9 SER A -20 UNP P33371 EXPRESSION TAG SEQADV 4BF9 SER A -19 UNP P33371 EXPRESSION TAG SEQADV 4BF9 HIS A -18 UNP P33371 EXPRESSION TAG SEQADV 4BF9 HIS A -17 UNP P33371 EXPRESSION TAG SEQADV 4BF9 HIS A -16 UNP P33371 EXPRESSION TAG SEQADV 4BF9 HIS A -15 UNP P33371 EXPRESSION TAG SEQADV 4BF9 HIS A -14 UNP P33371 EXPRESSION TAG SEQADV 4BF9 HIS A -13 UNP P33371 EXPRESSION TAG SEQADV 4BF9 SER A -12 UNP P33371 EXPRESSION TAG SEQADV 4BF9 SER A -11 UNP P33371 EXPRESSION TAG SEQADV 4BF9 GLY A -10 UNP P33371 EXPRESSION TAG SEQADV 4BF9 LEU A -9 UNP P33371 EXPRESSION TAG SEQADV 4BF9 VAL A -8 UNP P33371 EXPRESSION TAG SEQADV 4BF9 PRO A -7 UNP P33371 EXPRESSION TAG SEQADV 4BF9 ARG A -6 UNP P33371 EXPRESSION TAG SEQADV 4BF9 GLY A -5 UNP P33371 EXPRESSION TAG SEQADV 4BF9 SER A -4 UNP P33371 EXPRESSION TAG SEQADV 4BF9 HIS A -3 UNP P33371 EXPRESSION TAG SEQADV 4BF9 MSE A -2 UNP P33371 EXPRESSION TAG SEQADV 4BF9 ALA A -1 UNP P33371 EXPRESSION TAG SEQADV 4BF9 SER A 0 UNP P33371 EXPRESSION TAG SEQRES 1 A 338 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 338 LEU VAL PRO ARG GLY SER HIS MSE ALA SER MSE ARG VAL SEQRES 3 A 338 LEU LEU ALA PRO MSE GLU GLY VAL LEU ASP SER LEU VAL SEQRES 4 A 338 ARG GLU LEU LEU THR GLU VAL ASN ASP TYR ASP LEU CYS SEQRES 5 A 338 ILE THR GLU PHE VAL ARG VAL VAL ASP GLN LEU LEU PRO SEQRES 6 A 338 VAL LYS VAL PHE HIS ARG ILE CYS PRO GLU LEU GLN ASN SEQRES 7 A 338 ALA SER ARG THR PRO SER GLY THR LEU VAL ARG VAL GLN SEQRES 8 A 338 LEU LEU GLY GLN PHE PRO GLN TRP LEU ALA GLU ASN ALA SEQRES 9 A 338 ALA ARG ALA VAL GLU LEU GLY SER TRP GLY VAL ASP LEU SEQRES 10 A 338 ASN CYS GLY CYS PRO SER LYS THR VAL ASN GLY SER GLY SEQRES 11 A 338 GLY GLY ALA THR LEU LEU LYS ASP PRO GLU LEU ILE TYR SEQRES 12 A 338 GLN GLY ALA LYS ALA MSE ARG GLU ALA VAL PRO ALA HIS SEQRES 13 A 338 LEU PRO VAL SER VAL LYS VAL ARG LEU GLY TRP ASP SER SEQRES 14 A 338 GLY GLU LYS LYS PHE GLU ILE ALA ASP ALA VAL GLN GLN SEQRES 15 A 338 ALA GLY ALA THR GLU LEU VAL VAL HIS GLY ARG THR LYS SEQRES 16 A 338 GLU GLN GLY TYR ARG ALA GLU HIS ILE ASP TRP GLN ALA SEQRES 17 A 338 ILE GLY ASP ILE ARG GLN ARG LEU ASN ILE PRO VAL ILE SEQRES 18 A 338 ALA ASN GLY GLU ILE TRP ASP TRP GLN SER ALA GLN GLN SEQRES 19 A 338 CYS MSE ALA ILE SER GLY CYS ASP ALA VAL MSE ILE GLY SEQRES 20 A 338 ARG GLY ALA LEU ASN ILE PRO ASN LEU SER ARG VAL VAL SEQRES 21 A 338 LYS TYR ASN GLU PRO ARG MSE PRO TRP PRO GLU VAL VAL SEQRES 22 A 338 ALA LEU LEU GLN LYS TYR THR ARG LEU GLU LYS GLN GLY SEQRES 23 A 338 ASP THR GLY LEU TYR HIS VAL ALA ARG ILE LYS GLN TRP SEQRES 24 A 338 LEU SER TYR LEU ARG LYS GLU TYR ASP GLU ALA THR GLU SEQRES 25 A 338 LEU PHE GLN HIS VAL ARG VAL LEU ASN ASN SER PRO ASP SEQRES 26 A 338 ILE ALA ARG ALA ILE GLN ALA ILE ASP ILE GLU LYS LEU MODRES 4BF9 MSE A -2 MET SELENOMETHIONINE MODRES 4BF9 MSE A 1 MET SELENOMETHIONINE MODRES 4BF9 MSE A 8 MET SELENOMETHIONINE MODRES 4BF9 MSE A 126 MET SELENOMETHIONINE MODRES 4BF9 MSE A 213 MET SELENOMETHIONINE MODRES 4BF9 MSE A 222 MET SELENOMETHIONINE MODRES 4BF9 MSE A 244 MET SELENOMETHIONINE HET MSE A -2 8 HET MSE A 1 8 HET MSE A 8 8 HET MSE A 126 8 HET MSE A 213 8 HET MSE A 222 8 HET MSE A 244 8 HET FMN A 500 31 HETNAM MSE SELENOMETHIONINE HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 MSE 7(C5 H11 N O2 SE) FORMUL 3 FMN C17 H21 N4 O9 P FORMUL 4 HOH *104(H2 O) HELIX 1 1 ASP A 13 VAL A 23 1 11 HELIX 2 2 PRO A 42 CYS A 50 1 9 HELIX 3 3 PRO A 51 ALA A 56 5 6 HELIX 4 4 PHE A 73 LEU A 87 1 15 HELIX 5 5 GLY A 108 LYS A 114 5 7 HELIX 6 6 ASP A 115 VAL A 130 1 16 HELIX 7 7 LYS A 149 ALA A 160 1 12 HELIX 8 8 ARG A 177 ILE A 181 5 5 HELIX 9 9 ASP A 182 LEU A 193 1 12 HELIX 10 10 ASP A 205 GLY A 217 1 13 HELIX 11 11 ARG A 225 ILE A 230 1 6 HELIX 12 12 ASN A 232 ASN A 240 1 9 HELIX 13 13 PRO A 245 GLY A 263 1 19 HELIX 14 14 VAL A 270 ARG A 281 1 12 HELIX 15 15 ASP A 285 VAL A 296 1 12 HELIX 16 16 ASN A 299 ALA A 309 1 11 SHEET 1 AA 9 ARG A 2 LEU A 5 0 SHEET 2 AA 9 ALA A 220 ILE A 223 1 O VAL A 221 N LEU A 4 SHEET 3 AA 9 VAL A 197 ASN A 200 1 O ALA A 199 N MSE A 222 SHEET 4 AA 9 GLU A 164 HIS A 168 1 O LEU A 165 N ILE A 198 SHEET 5 AA 9 VAL A 136 ARG A 141 1 O VAL A 138 N VAL A 166 SHEET 6 AA 9 VAL A 92 CYS A 96 1 O VAL A 92 N SER A 137 SHEET 7 AA 9 VAL A 65 LEU A 70 1 O VAL A 67 N ASP A 93 SHEET 8 AA 9 LEU A 28 ARG A 35 1 O CYS A 29 N ARG A 66 SHEET 9 AA 9 ARG A 2 LEU A 5 1 O LEU A 5 N ILE A 30 LINK C MSE A -2 N ALA A -1 1555 1555 1.32 LINK N MSE A 1 C SER A 0 1555 1555 1.33 LINK C MSE A 1 N ARG A 2 1555 1555 1.32 LINK N MSE A 8 C PRO A 7 1555 1555 1.33 LINK C MSE A 8 N GLU A 9 1555 1555 1.32 LINK N MSE A 126 C ALA A 125 1555 1555 1.33 LINK C MSE A 126 N ARG A 127 1555 1555 1.34 LINK C MSE A 213 N ALA A 214 1555 1555 1.33 LINK N MSE A 213 C CYS A 212 1555 1555 1.33 LINK C MSE A 222 N ILE A 223 1555 1555 1.33 LINK N MSE A 222 C VAL A 221 1555 1555 1.33 LINK C MSE A 244 N PRO A 245 1555 1555 1.34 LINK N MSE A 244 C ARG A 243 1555 1555 1.33 SITE 1 AC1 18 ALA A 6 PRO A 7 MSE A 8 GLU A 9 SITE 2 AC1 18 PHE A 33 GLN A 68 ASN A 95 CYS A 98 SITE 3 AC1 18 LYS A 139 HIS A 168 TYR A 176 ASN A 200 SITE 4 AC1 18 GLY A 201 GLU A 202 GLY A 224 ARG A 225 SITE 5 AC1 18 HOH A2080 HOH A2082 CRYST1 94.140 94.140 119.680 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 0.010622 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008356 0.00000 HETATM 1 N MSE A -2 11.257 22.408 77.307 1.00 88.21 N ANISOU 1 N MSE A -2 12396 12273 8844 -259 1110 1150 N HETATM 2 CA MSE A -2 10.846 23.645 76.576 1.00 93.38 C ANISOU 2 CA MSE A -2 13020 12816 9643 -304 1133 855 C HETATM 3 C MSE A -2 11.946 24.143 75.656 1.00 85.07 C ANISOU 3 C MSE A -2 11866 11788 8667 -322 866 774 C HETATM 4 O MSE A -2 12.997 24.624 76.087 1.00 82.88 O ANISOU 4 O MSE A -2 11656 11693 8140 -394 680 749 O HETATM 5 CB MSE A -2 10.432 24.755 77.537 1.00109.30 C ANISOU 5 CB MSE A -2 15235 14910 11383 -400 1271 660 C HETATM 6 CG MSE A -2 9.407 25.669 76.854 1.00118.91 C ANISOU 6 CG MSE A -2 16396 15921 12862 -393 1440 428 C HETATM 7 SE MSE A -2 9.637 27.543 77.435 1.00139.74 SE ANISOU 7 SE MSE A -2 19236 18626 15233 -533 1470 90 SE HETATM 8 CE MSE A -2 11.379 27.936 76.581 1.00128.48 C ANISOU 8 CE MSE A -2 17714 17306 13796 -584 1062 59 C