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- PDB-3w9z: Crystal structure of DusC -

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Basic information

Entry
Database: PDB / ID: 3w9z
TitleCrystal structure of DusC
ComponentstRNA-dihydrouridine synthase C
KeywordsOXIDOREDUCTASE / Tim Barrel / reductase / tRNA
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 / tRNA-dihydrouridine(16) synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsChen, M. / Yu, J. / Tanaka, Y. / Tanaka, I. / Yao, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of dihydrouridine synthase C (DusC) from Escherichia coli
Authors: Chen, M. / Yu, J. / Tanaka, Y. / Tanaka, M. / Tanaka, I. / Yao, M.
History
DepositionApr 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-dihydrouridine synthase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6552
Polymers36,1981
Non-polymers4561
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.252, 93.252, 115.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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Components

#1: Protein tRNA-dihydrouridine synthase C


Mass: 36198.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2140, dusC, JW2128, yohI / Plasmid: pET-26(b) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P33371
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.4764.54
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion7.90.1M Tris pH7.9, 0.2M Na Acetate, 12% PEG 4000, VAPOR DIFFUSION, temperature 293K
2932vapor diffusion80.1M Imidazole pH8.0, 15% Isopropanol, 20% Glycerol , VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONSPring-8 BL41XU20.97914
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDOct 15, 2011
RAYONIX MX225HE2CCDNov 28, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979141
ReflectionResolution: 2.1→50 Å / Num. obs: 30439 / % possible obs: 99.9 % / Redundancy: 15.3 % / Rsym value: 0.063 / Net I/σ(I): 71.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 1489 / Rsym value: 0.707 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→49.097 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.7735 / SU ML: 0.26 / σ(F): 1.33 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1481 5.08 %RANDOM
Rwork0.2205 ---
obs0.2213 29181 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.6 Å2 / Biso mean: 58.0665 Å2 / Biso min: 30.89 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 31 109 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082381
X-RAY DIFFRACTIONf_angle_d1.1683235
X-RAY DIFFRACTIONf_chiral_restr0.076362
X-RAY DIFFRACTIONf_plane_restr0.006412
X-RAY DIFFRACTIONf_dihedral_angle_d15.737885
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0994-2.16720.33121310.3032551268298
2.1672-2.24470.37481370.31412489262697
2.2447-2.33450.36151400.29842416255694
2.3345-2.44080.33111350.29632363249892
2.4408-2.56950.33191160.27122383249992
2.5695-2.73040.2931280.26682427255593
2.7304-2.94120.28521250.25352444256994
2.9412-3.23720.28731380.24182516265496
3.2372-3.70550.20971560.21672597275399
3.7055-4.66790.19481230.180326932816100
4.6679-49.11060.20031520.200428212973100

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