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- PDB-9deu: Crystal structure of epoxyqueuosine reductase QueH in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9deu
TitleCrystal structure of epoxyqueuosine reductase QueH in complex with queuosine
ComponentsEpoxyqueuosine reductase QueH
KeywordsMETAL BINDING PROTEIN / Queuosine Biosynthesis / Epoxyqueuosine Reductase / Metalloenzyme
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
Chem-56B / IRON/SULFUR CLUSTER / Epoxyqueuosine reductase QueH
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 29, 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)23,4915
Polymers22,5491
Non-polymers9424
Water1,02757
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)53.647, 105.194, 73.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

21A-357-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 22548.875 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 61 molecules

#2: Chemical ChemComp-56B / 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one


Type: RNA linking / Mass: 489.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24N5O10P / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.72 %
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: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.7→36.9 Å / Num. obs: 22745 / % possible obs: 97.68 % / Redundancy: 11.6 % / Biso Wilson estimate: 30.54 Å2 / CC1/2: 0.999 / Net I/σ(I): 24.86
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 1901 / CC1/2: 0.706

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.9 Å / SU ML: 0.1899 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 1212 5.33 %
Rwork0.2194 21530 -
obs0.2199 22742 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 42 57 1421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02391398
X-RAY DIFFRACTIONf_angle_d1.42181891
X-RAY DIFFRACTIONf_chiral_restr0.507202
X-RAY DIFFRACTIONf_plane_restr0.0452234
X-RAY DIFFRACTIONf_dihedral_angle_d15.204517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.31851070.26732011X-RAY DIFFRACTION83.42
1.77-1.850.23471500.23522316X-RAY DIFFRACTION95.77
1.85-1.950.2681350.23222406X-RAY DIFFRACTION100
1.95-2.070.24531320.222417X-RAY DIFFRACTION99.92
2.07-2.230.23021220.21822450X-RAY DIFFRACTION100
2.23-2.460.2561570.21972420X-RAY DIFFRACTION100
2.46-2.810.21011360.22992448X-RAY DIFFRACTION100
2.81-3.540.24561530.21442456X-RAY DIFFRACTION99.92
3.54-36.90.20681200.21462606X-RAY DIFFRACTION99.96

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