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- PDB-8b02: Crystal structure of the dsRBD domain of tRNA-dihydrouridine(20) ... -

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Basic information

Entry
Database: PDB / ID: 8b02
TitleCrystal structure of the dsRBD domain of tRNA-dihydrouridine(20) synthase from Amphimedon queenslandica
ComponentsDRBM domain-containing protein
KeywordsRNA BINDING PROTEIN / DOUBLE-STRANDED RNA-BINDING DOMAIN / DIHYDROURIDINE SYNTHASE 2
Function / homology
Function and homology information


tRNA dihydrouridine synthase activity / flavin adenine dinucleotide binding / tRNA binding
Similarity search - Function
DUS2, double-stranded RNA binding domain / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Aldolase-type TIM barrel
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / DRBM domain-containing protein
Similarity search - Component
Biological speciesAmphimedon queenslandica (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.676 Å
AuthorsPecqueur, L. / Faivre, B. / Hamdane, D.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE92-030 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0011-01 France
CitationJournal: Biomolecules / Year: 2022
Title: Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family.
Authors: Lombard, M. / Reed, C.J. / Pecqueur, L. / Faivre, B. / Toubdji, S. / Sudol, C. / Bregeon, D. / de Crecy-Lagard, V. / Hamdane, D.
History
DepositionSep 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 4, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DRBM domain-containing protein
B: DRBM domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6779
Polymers26,1742
Non-polymers5037
Water2,504139
1
A: DRBM domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2003
Polymers13,0871
Non-polymers1142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DRBM domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4776
Polymers13,0871
Non-polymers3905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.077, 56.895, 63.587
Angle α, β, γ (deg.)90, 93.05, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DRBM domain-containing protein


Mass: 13086.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphimedon queenslandica (invertebrata)
Gene: 100640958 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1X7V4K0
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 1.4 M tri-sodium citrate, 15 mg/ml protein in 50 mM Tris, pH 8 300 mM NaCl 5mM mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.676→42.373 Å / Num. obs: 23361 / % possible obs: 97.9 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.051 / Rrim(I) all: 0.09 / Net I/σ(I): 7.8
Reflection shellResolution: 1.676→1.705 Å / Redundancy: 2 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 963 / CC1/2: 0.351 / Rpim(I) all: 0.762 / Rrim(I) all: 1.245 / % possible all: 79.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
autoPROC1.0.5data reduction
XDSJan 10, 2022 (BUILT 20220220)data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wft

4wft


Resolution: 1.676→29.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1170 -RANDOM
Rwork0.2035 ---
obs0.2047 23356 97.8 %-
Displacement parametersBiso mean: 28.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.9139 Å20 Å2-1.3752 Å2
2---1.5478 Å20 Å2
3---3.4616 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.676→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 28 139 1715
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091641HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022234HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d572SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes271HARMONIC5
X-RAY DIFFRACTIONt_it1641HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion232SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1502SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion12.48
LS refinement shellResolution: 1.68→1.69 Å
RfactorNum. reflection% reflection
Rfree0.3688 33 -
Rwork0.3182 --
obs0.3218 468 73.43 %

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