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- PDB-9d86: Crystal structure of epoxyqueuosine reductase QueH C9S mutant fro... -

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Basic information

Entry
Database: PDB / ID: 9d86
TitleCrystal structure of epoxyqueuosine reductase QueH C9S mutant from Thermotoga maritima
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
IRON/SULFUR CLUSTER / Epoxyqueuosine reductase QueH
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 18, 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)22,8842
Polymers22,5331
Non-polymers3521
Water63135
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)52.742, 104.970, 73.678
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

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Components

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


Mass: 22532.809 Da / Num. of mol.: 1 / Mutation: C9S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris-HCl pH5.5, 0.2 M lithium sulfate monohydrate, 25% (w/v) polyethylene glycerol (PEG) 3350, 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: 1.03321 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.88→30.15 Å / Num. obs: 16852 / % possible obs: 99.69 % / Redundancy: 12.6 % / Biso Wilson estimate: 38.34 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.51
Reflection shellResolution: 1.88→1.951 Å / Num. unique obs: 1608 / CC1/2: 0.605

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→30.15 Å / SU ML: 0.2878 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8796
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2534 822 4.88 %
Rwork0.2056 16029 -
obs0.2077 16851 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.62 Å2
Refinement stepCycle: LAST / Resolution: 1.88→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 8 35 1515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961516
X-RAY DIFFRACTIONf_angle_d1.02582043
X-RAY DIFFRACTIONf_chiral_restr0.0571214
X-RAY DIFFRACTIONf_plane_restr0.0115261
X-RAY DIFFRACTIONf_dihedral_angle_d5.4411203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-20.40441290.32492574X-RAY DIFFRACTION98.47
2-2.160.29321320.24122653X-RAY DIFFRACTION100
2.16-2.370.25311400.23142648X-RAY DIFFRACTION100
2.37-2.720.27221570.22632637X-RAY DIFFRACTION100
2.72-3.420.27211250.2192702X-RAY DIFFRACTION100
3.42-30.150.22261390.17822815X-RAY DIFFRACTION99.9

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