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Yorodumi- PDB-7y7n: Crystal structure of DUF371 domain-containing protein from Methan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y7n | ||||||
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Title | Crystal structure of DUF371 domain-containing protein from Methanobrevibacter ruminantium | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / unknow function | ||||||
Function / homology | Protein of unknown function DUF371 / Mth639-like domain superfamily / Domain of unknown function (DUF371) / DUF371 domain-containing protein Function and homology information | ||||||
Biological species | Methanobrevibacter ruminantium (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 Å | ||||||
Authors | Yang, Q. / Lai, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of DUF371 domain-containing protein from methanobrevibacter ruminantium Authors: Yang, Q. / Lai, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y7n.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y7n.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 7y7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y7n_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 7y7n_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 7y7n_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 7y7n_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/7y7n ftp://data.pdbj.org/pub/pdb/validation_reports/y7/7y7n | HTTPS FTP |
-Related structure data
Related structure data | 3cbnS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15417.749 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanobrevibacter ruminantium (archaea) Strain: ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1 / Gene: mru_1462 / Production host: Escherichia (bacteria) / References: UniProt: D3E451 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 12.00% w/v Polyethylene glycol 8,000,5.00% w/v Glycerol,100 mM Potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97919 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→44.72 Å / Num. obs: 16164 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.043 / Rrim(I) all: 0.1 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.597 / Num. unique obs: 864 / CC1/2: 0.837 / Rpim(I) all: 0.763 / Rrim(I) all: 0.098 |
-Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3cbn Resolution: 1.764→44.716 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.099 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.131 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.081 Å2
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Refinement step | Cycle: LAST / Resolution: 1.764→44.716 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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