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Yorodumi- PDB-7lc5: Crystal structure of epoxyqueuosine reductase QueH from Thermotog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lc5 | ||||||
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Title | Crystal structure of epoxyqueuosine reductase QueH from Thermotoga maritima | ||||||
Components | Epoxyqueuosine reductase QueH | ||||||
Keywords | OXIDOREDUCTASE / Epoxyqueuosine Reductase / QueH / Iron-Sulfur Cluster / Queuosine / tRNA | ||||||
Function / homology | Function and homology information epoxyqueuosine reductase / epoxyqueuosine reductase activity / queuosine biosynthetic process / tRNA processing / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Li, Q. / Bruner, S.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lc5.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lc5.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lc5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7lc5_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7lc5_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7lc5_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/7lc5 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/7lc5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.37 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2018 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→47.49 Å
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Refine LS restraints |
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LS refinement shell |
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