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- PDB-7lc5: Crystal structure of epoxyqueuosine reductase QueH from Thermotog... -

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Basic information

Entry
Database: PDB / ID: 7lc5
TitleCrystal structure of epoxyqueuosine reductase QueH from Thermotoga maritima
ComponentsEpoxyqueuosine reductase QueH
KeywordsOXIDOREDUCTASE / Epoxyqueuosine Reductase / QueH / Iron-Sulfur Cluster / Queuosine / tRNA
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 / SAD / Resolution: 1.5 Å
AuthorsLi, Q. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM70641 United States
CitationJournal: Biochemistry / Year: 2021
Title: Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme.
Authors: Li, Q. / Zallot, R. / MacTavish, B.S. / Montoya, A. / Payan, D.J. / Hu, Y. / Gerlt, J.A. / Angerhofer, A. / de Crecy-Lagard, V. / Bruner, S.D.
History
DepositionJan 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)22,9924
Polymers22,5491
Non-polymers4433
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-45 kcal/mol
Surface area8790 Å2
Unit cell
Length a, b, c (Å)53.224, 105.181, 73.899
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: 22548.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / 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.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris, pH 5.5, 200 mM lithium sulfate monohydrate, 25% PEG3350

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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 PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2018
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.497→47.49 Å / Num. obs: 33575 / % possible obs: 99.33 % / Redundancy: 13 % / Biso Wilson estimate: 22.33 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04388 / Rpim(I) all: 0.01258 / Rrim(I) all: 0.04569 / Net I/σ(I): 36.83
Reflection shellResolution: 1.497→1.551 Å / Rmerge(I) obs: 0.7082 / Mean I/σ(I) obs: 4.85 / Num. unique obs: 3276 / CC1/2: 0.929 / CC star: 0.982 / Rpim(I) all: 0.207 / Rrim(I) all: 0.7385

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→47.49 Å / SU ML: 0.157 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 1679 5 %
Rwork0.1955 31884 -
obs0.1963 33563 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.39 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 10 98 1580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641516
X-RAY DIFFRACTIONf_angle_d0.80482043
X-RAY DIFFRACTIONf_chiral_restr0.0784214
X-RAY DIFFRACTIONf_plane_restr0.0043261
X-RAY DIFFRACTIONf_dihedral_angle_d8.205573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.23661530.24072573X-RAY DIFFRACTION97.99
1.54-1.590.23571290.22132621X-RAY DIFFRACTION98.67
1.59-1.650.2311290.20432599X-RAY DIFFRACTION98.91
1.65-1.710.25061330.19932644X-RAY DIFFRACTION99.14
1.71-1.790.21571560.19522607X-RAY DIFFRACTION99.21
1.79-1.890.22081220.19262645X-RAY DIFFRACTION99.35
1.89-20.22951350.20292633X-RAY DIFFRACTION99.64
2-2.160.21481360.19772674X-RAY DIFFRACTION99.68
2.16-2.380.22061380.19462676X-RAY DIFFRACTION99.82
2.38-2.720.21351400.20012688X-RAY DIFFRACTION99.96
2.72-3.430.21861510.20152711X-RAY DIFFRACTION100
3.43-47.490.19291570.18442813X-RAY DIFFRACTION99.56

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