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- PDB-9dco: Crystal structure of epoxyqueuosine reductase QueH D13N mutant fr... -

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Basic information

Entry
Database: PDB / ID: 9dco
TitleCrystal structure of epoxyqueuosine reductase QueH D13N mutant from Thermotoga maritima
ComponentsEpoxyqueuosine reductase QueH
KeywordsMETAL BINDING PROTEIN / Queuosine Biosynthesis / Epoxyqueuosine Reductase
Function / homology
Function and homology information


epoxyqueuosine reductase / epoxyqueuosine reductase activity / tRNA modification / tRNA queuosine(34) biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Epoxyqueuosine reductase QueH / Epoxyqueuosine reductase QueH
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Epoxyqueuosine reductase QueH
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsHu, Y. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM70641 United States
CitationJournal: Biochemistry / Year: 2025
Title: Mechanism of Catalysis and Substrate Binding of Epoxyqueuosine Reductase in the Biosynthetic Pathway to Queuosine-Modified tRNA.
Authors: Hu, Y. / Jaroch, M. / Sun, G. / Dedon, P.C. / de Crecy-Lagard, V. / Bruner, S.D.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epoxyqueuosine reductase QueH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0004
Polymers22,5481
Non-polymers4533
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.868, 40.133, 120.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Epoxyqueuosine reductase QueH / Queuosine biosynthesis protein QueH


Mass: 22547.889 Da / Num. of mol.: 1 / Mutation: D13N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: queH, TM_0731 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WZJ0, epoxyqueuosine reductase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris, pH 5.5, 200 mM lithium sulfate monohydrate, 25% PEG3350, 10 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.11→28.36 Å / Num. obs: 11404 / % possible obs: 99.73 % / Redundancy: 6.8 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.65
Reflection shellResolution: 2.11→2.185 Å / Num. unique obs: 1097 / CC1/2: 0.689

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→28.36 Å / SU ML: 0.3675 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3084 574 5.03 %
Rwork0.2361 10830 -
obs0.2396 11404 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.29 Å2
Refinement stepCycle: LAST / Resolution: 2.11→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 10 40 1522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02691516
X-RAY DIFFRACTIONf_angle_d1.99012043
X-RAY DIFFRACTIONf_chiral_restr0.1355214
X-RAY DIFFRACTIONf_plane_restr0.0183261
X-RAY DIFFRACTIONf_dihedral_angle_d17.8852573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.320.3241580.26162571X-RAY DIFFRACTION97.39
2.32-2.650.3751400.25282702X-RAY DIFFRACTION100
2.65-3.340.30321280.25082716X-RAY DIFFRACTION99.86
3.34-28.360.28461480.21792841X-RAY DIFFRACTION99.67

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