HEADER OXIDOREDUCTASE 16-MAR-13 4BFA TITLE CRYSTAL STRUCTURE OF E. COLI DIHYDROURIDINE SYNTHASE C (DUSC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA-DIHYDROURIDINE SYNTHASE C; COMPND 3 CHAIN: A, B; 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 OXIDOREDUCTASE, TRNA MODIFICATION EXPDTA X-RAY DIFFRACTION AUTHOR R.T.BYRNE,F.WHELAN,A.KONEVEGA,N.AZIZ,M.RODNINA,A.A.ANTSON REVDAT 4 27-MAY-15 4BFA 1 JRNL REVDAT 3 13-MAY-15 4BFA 1 JRNL REVDAT 2 22-APR-15 4BFA 1 JRNL REVDAT 1 06-NOV-13 4BFA 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. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0024 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.91 REMARK 3 NUMBER OF REFLECTIONS : 94507 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) : 0.13655 REMARK 3 R VALUE (WORKING SET) : 0.13443 REMARK 3 FREE R VALUE : 0.17673 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 5013 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) : 1.650 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.693 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6867 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.179 REMARK 3 BIN FREE R VALUE SET COUNT : 407 REMARK 3 BIN FREE R VALUE : 0.239 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4970 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 611 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.619 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.88 REMARK 3 B22 (A**2) : 0.71 REMARK 3 B33 (A**2) : 0.17 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.143 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5163 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5020 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7033 ; 1.278 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11502 ; 0.791 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 645 ; 5.494 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 239 ;36.309 ;23.891 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 884 ;12.056 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;16.519 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 785 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6057 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1177 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 10183 ; 3.193 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 225 ;37.306 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 10462 ;14.828 ; 5.000 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 : NULL 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 REFINED INDIVIDUALLY. REMARK 4 REMARK 4 4BFA 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-56170. 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 : 8.5 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 : 99677 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.65 REMARK 200 RESOLUTION RANGE LOW (A) : 60.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.3 REMARK 200 R MERGE (I) : 0.10 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.6 REMARK 200 R MERGE FOR SHELL (I) : 0.71 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.60 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: PDB ENTRY 4BF9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOLECULAR DIMENSION MORPHEUS REMARK 280 SCREEN CONDITION C10 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 34.27000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.94800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.97650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.94800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.27000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.97650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 -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 465 MET A -2 REMARK 465 MET B -22 REMARK 465 GLY B -21 REMARK 465 SER B -20 REMARK 465 SER B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 SER B -12 REMARK 465 SER B -11 REMARK 465 GLY B -10 REMARK 465 LEU B -9 REMARK 465 VAL B -8 REMARK 465 PRO B -7 REMARK 465 ARG B -6 REMARK 465 GLY B -5 REMARK 465 SER B -4 REMARK 465 HIS B -3 REMARK 465 MET B -2 REMARK 465 CYS B 98 REMARK 465 PRO B 99 REMARK 465 SER B 100 REMARK 465 LYS B 101 REMARK 465 THR B 102 REMARK 465 VAL B 103 REMARK 465 ASN B 104 REMARK 465 GLY B 105 REMARK 465 SER B 106 REMARK 465 GLY B 107 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 101 CG CD CE NZ REMARK 470 LYS A 314 CG CD CE NZ REMARK 470 GLU B 148 CG CD OE1 OE2 REMARK 470 GLU B 173 CG CD OE1 OE2 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 OD1 ASP A 302 NH2 ARG A 305 1.97 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 VAL A 11 -61.86 -132.11 REMARK 500 VAL A 37 -92.73 -115.27 REMARK 500 ASN A 104 -75.16 -119.16 REMARK 500 TRP A 144 -73.95 -88.36 REMARK 500 VAL B 11 -64.28 -130.60 REMARK 500 VAL B 37 -84.47 -119.18 REMARK 500 TRP B 144 -78.28 -84.19 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 700 REMARK 700 THE SHEETS PRESENTED AS "BA" 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 A1316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B1316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A1319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B1319 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BF9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI DIHYDROURIDINE SYNTHASE C REMARK 900 (DUSC) (SELENOMETHIONINE DERIVATIVE) DBREF 4BFA A 1 315 UNP P33371 DUSC_ECOLI 1 315 DBREF 4BFA B 1 315 UNP P33371 DUSC_ECOLI 1 315 SEQADV 4BFA MET A -22 UNP P33371 EXPRESSION TAG SEQADV 4BFA GLY A -21 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER A -20 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER A -19 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS A -18 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS A -17 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS A -16 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS A -15 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS A -14 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS A -13 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER A -12 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER A -11 UNP P33371 EXPRESSION TAG SEQADV 4BFA GLY A -10 UNP P33371 EXPRESSION TAG SEQADV 4BFA LEU A -9 UNP P33371 EXPRESSION TAG SEQADV 4BFA VAL A -8 UNP P33371 EXPRESSION TAG SEQADV 4BFA PRO A -7 UNP P33371 EXPRESSION TAG SEQADV 4BFA ARG A -6 UNP P33371 EXPRESSION TAG SEQADV 4BFA GLY A -5 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER A -4 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS A -3 UNP P33371 EXPRESSION TAG SEQADV 4BFA MET A -2 UNP P33371 EXPRESSION TAG SEQADV 4BFA ALA A -1 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER A 0 UNP P33371 EXPRESSION TAG SEQADV 4BFA MET B -22 UNP P33371 EXPRESSION TAG SEQADV 4BFA GLY B -21 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER B -20 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER B -19 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS B -18 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS B -17 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS B -16 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS B -15 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS B -14 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS B -13 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER B -12 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER B -11 UNP P33371 EXPRESSION TAG SEQADV 4BFA GLY B -10 UNP P33371 EXPRESSION TAG SEQADV 4BFA LEU B -9 UNP P33371 EXPRESSION TAG SEQADV 4BFA VAL B -8 UNP P33371 EXPRESSION TAG SEQADV 4BFA PRO B -7 UNP P33371 EXPRESSION TAG SEQADV 4BFA ARG B -6 UNP P33371 EXPRESSION TAG SEQADV 4BFA GLY B -5 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER B -4 UNP P33371 EXPRESSION TAG SEQADV 4BFA HIS B -3 UNP P33371 EXPRESSION TAG SEQADV 4BFA MET B -2 UNP P33371 EXPRESSION TAG SEQADV 4BFA ALA B -1 UNP P33371 EXPRESSION TAG SEQADV 4BFA SER B 0 UNP P33371 EXPRESSION TAG SEQRES 1 A 338 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 338 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET ARG VAL SEQRES 3 A 338 LEU LEU ALA PRO MET 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 MET 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 MET ALA ILE SER GLY CYS ASP ALA VAL MET 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 MET 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 SEQRES 1 B 338 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 338 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET ARG VAL SEQRES 3 B 338 LEU LEU ALA PRO MET GLU GLY VAL LEU ASP SER LEU VAL SEQRES 4 B 338 ARG GLU LEU LEU THR GLU VAL ASN ASP TYR ASP LEU CYS SEQRES 5 B 338 ILE THR GLU PHE VAL ARG VAL VAL ASP GLN LEU LEU PRO SEQRES 6 B 338 VAL LYS VAL PHE HIS ARG ILE CYS PRO GLU LEU GLN ASN SEQRES 7 B 338 ALA SER ARG THR PRO SER GLY THR LEU VAL ARG VAL GLN SEQRES 8 B 338 LEU LEU GLY GLN PHE PRO GLN TRP LEU ALA GLU ASN ALA SEQRES 9 B 338 ALA ARG ALA VAL GLU LEU GLY SER TRP GLY VAL ASP LEU SEQRES 10 B 338 ASN CYS GLY CYS PRO SER LYS THR VAL ASN GLY SER GLY SEQRES 11 B 338 GLY GLY ALA THR LEU LEU LYS ASP PRO GLU LEU ILE TYR SEQRES 12 B 338 GLN GLY ALA LYS ALA MET ARG GLU ALA VAL PRO ALA HIS SEQRES 13 B 338 LEU PRO VAL SER VAL LYS VAL ARG LEU GLY TRP ASP SER SEQRES 14 B 338 GLY GLU LYS LYS PHE GLU ILE ALA ASP ALA VAL GLN GLN SEQRES 15 B 338 ALA GLY ALA THR GLU LEU VAL VAL HIS GLY ARG THR LYS SEQRES 16 B 338 GLU GLN GLY TYR ARG ALA GLU HIS ILE ASP TRP GLN ALA SEQRES 17 B 338 ILE GLY ASP ILE ARG GLN ARG LEU ASN ILE PRO VAL ILE SEQRES 18 B 338 ALA ASN GLY GLU ILE TRP ASP TRP GLN SER ALA GLN GLN SEQRES 19 B 338 CYS MET ALA ILE SER GLY CYS ASP ALA VAL MET ILE GLY SEQRES 20 B 338 ARG GLY ALA LEU ASN ILE PRO ASN LEU SER ARG VAL VAL SEQRES 21 B 338 LYS TYR ASN GLU PRO ARG MET PRO TRP PRO GLU VAL VAL SEQRES 22 B 338 ALA LEU LEU GLN LYS TYR THR ARG LEU GLU LYS GLN GLY SEQRES 23 B 338 ASP THR GLY LEU TYR HIS VAL ALA ARG ILE LYS GLN TRP SEQRES 24 B 338 LEU SER TYR LEU ARG LYS GLU TYR ASP GLU ALA THR GLU SEQRES 25 B 338 LEU PHE GLN HIS VAL ARG VAL LEU ASN ASN SER PRO ASP SEQRES 26 B 338 ILE ALA ARG ALA ILE GLN ALA ILE ASP ILE GLU LYS LEU HET FMN A1316 31 HET FMN B1316 31 HET EDO A1317 4 HET EDO A1318 4 HET EDO B1317 4 HET EDO B1318 4 HET NO3 A1319 4 HET NO3 B1319 4 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM NO3 NITRATE ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 EDO 4(C2 H6 O2) FORMUL 5 NO3 2(N O3 1-) FORMUL 6 HOH *611(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 GLY A 224 ILE A 230 1 7 HELIX 12 12 ASN A 232 ASN A 240 1 9 HELIX 13 13 PRO A 245 LEU A 259 1 15 HELIX 14 14 LEU A 267 ARG A 281 1 15 HELIX 15 15 TYR A 284 ARG A 295 1 12 HELIX 16 16 ASN A 299 ILE A 310 1 12 HELIX 17 17 ASP B 13 VAL B 23 1 11 HELIX 18 18 PRO B 42 CYS B 50 1 9 HELIX 19 19 PRO B 51 ALA B 56 5 6 HELIX 20 20 PHE B 73 LEU B 87 1 15 HELIX 21 21 GLY B 108 LYS B 114 5 7 HELIX 22 22 ASP B 115 VAL B 130 1 16 HELIX 23 23 LYS B 149 ALA B 160 1 12 HELIX 24 24 ARG B 177 ILE B 181 5 5 HELIX 25 25 ASP B 182 LEU B 193 1 12 HELIX 26 26 ASP B 205 GLY B 217 1 13 HELIX 27 27 GLY B 224 ILE B 230 1 7 HELIX 28 28 ASN B 232 ASN B 240 1 9 HELIX 29 29 PRO B 245 LEU B 259 1 15 HELIX 30 30 LEU B 267 ARG B 281 1 15 HELIX 31 31 TYR B 284 ARG B 295 1 12 HELIX 32 32 ASN B 299 ALA B 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 MET 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 SHEET 1 BA 9 ARG B 2 LEU B 5 0 SHEET 2 BA 9 ALA B 220 ILE B 223 1 O VAL B 221 N LEU B 4 SHEET 3 BA 9 VAL B 197 ASN B 200 1 O ALA B 199 N MET B 222 SHEET 4 BA 9 GLU B 164 THR B 171 1 O LEU B 165 N ILE B 198 SHEET 5 BA 9 VAL B 136 GLY B 143 1 O VAL B 138 N VAL B 166 SHEET 6 BA 9 VAL B 92 ASN B 95 1 O VAL B 92 N SER B 137 SHEET 7 BA 9 VAL B 65 LEU B 70 1 O VAL B 67 N ASP B 93 SHEET 8 BA 9 LEU B 28 ARG B 35 1 O CYS B 29 N ARG B 66 SHEET 9 BA 9 ARG B 2 LEU B 5 1 O LEU B 5 N ILE B 30 SITE 1 AC1 20 ALA A 6 PRO A 7 MET A 8 GLU A 9 SITE 2 AC1 20 PHE A 33 GLN A 68 ASN A 95 CYS A 98 SITE 3 AC1 20 LYS A 139 HIS A 168 TYR A 176 ASN A 200 SITE 4 AC1 20 GLY A 201 GLU A 202 GLY A 224 ARG A 225 SITE 5 AC1 20 HOH A2132 HOH A2215 HOH A2219 ARG B 177 SITE 1 AC2 19 ARG A 177 ALA B 6 PRO B 7 MET B 8 SITE 2 AC2 19 GLU B 9 PHE B 33 GLN B 68 ASN B 95 SITE 3 AC2 19 LYS B 139 HIS B 168 TYR B 176 ASN B 200 SITE 4 AC2 19 GLY B 201 GLU B 202 GLY B 224 ARG B 225 SITE 5 AC2 19 HOH B2132 HOH B2196 HOH B2199 SITE 1 AC3 7 TRP A 183 GLN A 211 HOH A2196 HOH A2216 SITE 2 AC3 7 HOH A2303 ARG B 281 THR B 288 SITE 1 AC4 7 ARG A 225 ASN A 229 TYR A 279 LYS A 282 SITE 2 AC4 7 HOH A2236 HOH A2285 GLU B 179 SITE 1 AC5 4 ALA A 132 ARG B 2 ASP B 27 TRP B 90 SITE 1 AC6 4 ASP B 155 GLN B 158 GLN B 159 HOH B2306 SITE 1 AC7 9 ASP A 182 TRP A 183 GLN A 184 HOH A2303 SITE 2 AC7 9 HOH A2304 ARG B 281 PHE B 291 GLN B 292 SITE 3 AC7 9 ARG B 295 SITE 1 AC8 8 ARG A 281 GLN A 292 ARG A 295 HOH A2289 SITE 2 AC8 8 ILE B 181 ASP B 182 TRP B 183 GLN B 184 CRYST1 68.540 99.953 119.896 90.00 90.00 90.00 P 21 21 21 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 0.014590 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010005 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008341 0.00000 MASTER 392 0 8 32 18 0 21 6 0 0 0 52 END