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Yorodumi- PDB-7qbk: Crystal structure of a second homolog of R2-like ligand-binding o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qbk | |||||||||||||||
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Title | Crystal structure of a second homolog of R2-like ligand-binding oxidase in Sulfolobus acidocaldarius (SaR2loxII) | |||||||||||||||
Components | R2-like ligand-binding oxidase (homolog II) from Sulfolobus acidocaldarius | |||||||||||||||
Keywords | OXIDOREDUCTASE / R2LOX / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN / FERRITIN-LIKE SUPERFAMILY | |||||||||||||||
Function / homology | Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / deoxyribonucleotide biosynthetic process / Ribonucleotide reductase-like / Ferritin-like superfamily / oxidoreductase activity / : / MANGANESE (III) ION / Uncharacterized protein Function and homology information | |||||||||||||||
Biological species | Sulfolobus acidocaldarius DSM 639 (acidophilic) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | |||||||||||||||
Authors | Lebrette, H. / Diamanti, R. / Srinivas, V. / Hogbom, M. | |||||||||||||||
Funding support | Sweden, 4items
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Citation | Journal: Febs Lett. / Year: 2022 Title: Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase. Authors: Diamanti, R. / Srinivas, V. / Johansson, A.I. / Nordstrom, A. / Griese, J.J. / Lebrette, H. / Hogbom, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qbk.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qbk.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 7qbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/7qbk ftp://data.pdbj.org/pub/pdb/validation_reports/qb/7qbk | HTTPS FTP |
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-Related structure data
Related structure data | 7qbpC 4hr0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37060.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic) Gene: Saci_1112 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4J9R6 |
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#2: Chemical | ChemComp-MN3 / |
#3: Chemical | ChemComp-FE / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 24% (w/v) polyethylene glycol 1500, 5% (v/v) formamide, 40 mM sodium propionate, 20 mM sodium cacodylate trihydrate, 40 mM bis-tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→41.91 Å / Num. obs: 17196 / % possible obs: 91.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.35 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1587 / Rpim(I) all: 0.0948 / Rrim(I) all: 0.1858 / Net I/σ(I): 6.67 |
Reflection shell | Resolution: 2.26→2.341 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.442 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 1739 / CC1/2: 0.398 / CC star: 0.755 / Rpim(I) all: 0.8499 / Rrim(I) all: 1.683 / % possible all: 93.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4hr0 Resolution: 2.26→41.91 Å / SU ML: 0.3396 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.3506 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: 46.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→41.91 Å
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Refine LS restraints |
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LS refinement shell |
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