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- PDB-4bfa: Crystal structure of E. coli dihydrouridine synthase C (DusC) -

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Basic information

Entry
Database: PDB / ID: 4bfa
TitleCrystal structure of E. coli dihydrouridine synthase C (DusC)
ComponentsTRNA-DIHYDROURIDINE SYNTHASE C
KeywordsOXIDOREDUCTASE / TRNA MODIFICATION
Function / homology
Function and homology information


tRNA-dihydrouridine16 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / FMN binding / flavin adenine dinucleotide binding / tRNA binding
Similarity search - Function
Dihydrouridine synthase, C-terminal recognition domain / tRNA-dihydrouridine(16) synthase / tRNA-dihydrouridine(16) synthase, C-terminal / tRNA-dihydrouridine synthase / Bacteriocin As-48; Chain A / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Aldolase class I ...Dihydrouridine synthase, C-terminal recognition domain / tRNA-dihydrouridine(16) synthase / tRNA-dihydrouridine(16) synthase, C-terminal / tRNA-dihydrouridine synthase / Bacteriocin As-48; Chain A / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NITRATE ION / tRNA-dihydrouridine(16) synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsByrne, R.T. / Whelan, F. / Konevega, A. / Aziz, N. / Rodnina, M. / Antson, A.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Major Reorientation of tRNA Substrates Defines Specificity of Dihydrouridine Synthases.
Authors: Byrne, R.T. / Jenkins, H.T. / Peters, D.T. / Whelan, F. / Stowell, J. / Aziz, N. / Kasatsky, P. / Rodnina, M.V. / Koonin, E.V. / Konevega, A.L. / Antson, A.A.
History
DepositionMar 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3May 27, 2015Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRNA-DIHYDROURIDINE SYNTHASE C
B: TRNA-DIHYDROURIDINE SYNTHASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,68710
Polymers75,4022
Non-polymers1,2858
Water11,007611
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A: TRNA-DIHYDROURIDINE SYNTHASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3445
Polymers37,7011
Non-polymers6424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRNA-DIHYDROURIDINE SYNTHASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3445
Polymers37,7011
Non-polymers6424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.540, 99.953, 119.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRNA-DIHYDROURIDINE SYNTHASE C / DIHYDROURIDINE SYNTHASE C


Mass: 37701.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Strain: MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: P33371, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 8.5
Details: MOLECULAR DIMENSION MORPHEUS SCREEN CONDITION C10, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9808
DetectorType: ADSC CCD / Detector: CCD / Date: May 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9808 Å / Relative weight: 1
ReflectionResolution: 1.65→60 Å / Num. obs: 99677 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0024refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BF9

4bf9


Resolution: 1.65→51.13 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.143 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.17673 5013 5 %RANDOM
Rwork0.13443 ---
obs0.13655 94507 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2--0.71 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.65→51.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 86 611 5591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025163
X-RAY DIFFRACTIONr_bond_other_d0.0010.025020
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9767033
X-RAY DIFFRACTIONr_angle_other_deg0.791311502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30923.891239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05615884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5191546
X-RAY DIFFRACTIONr_chiral_restr0.0730.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216057
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021177
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.193310183
X-RAY DIFFRACTIONr_sphericity_free37.3065225
X-RAY DIFFRACTIONr_sphericity_bonded14.828510462
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 407 -
Rwork0.179 6867 -
obs--99.9 %

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