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Yorodumi- PDB-6l7q: Crystal structure of a hypothetical protein PYCH_01220 derived fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l7q | ||||||
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Title | Crystal structure of a hypothetical protein PYCH_01220 derived from Pyrococcus yayanosii | ||||||
Components | hypothetical protein | ||||||
Keywords | UNKNOWN FUNCTION / cytosolic protein / hypothetical protein | ||||||
Function / homology | Uncharacterized protein Function and homology information | ||||||
Biological species | Pyrococcus yayanosii | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.16 Å | ||||||
Authors | Jeon, J.-H. / Noh, H. / Oh, B.-H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Proteins / Year: 2021 Title: Crystal structure of PYCH_01220 from Pyrococcus yayanosii potentially involved in binding nucleic acid. Authors: Noh, H. / Jeon, J.H. / Kim, Y.G. / Oh, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l7q.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l7q.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 6l7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l7q_validation.pdf.gz | 418.4 KB | Display | wwPDB validaton report |
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Full document | 6l7q_full_validation.pdf.gz | 420.4 KB | Display | |
Data in XML | 6l7q_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 6l7q_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/6l7q ftp://data.pdbj.org/pub/pdb/validation_reports/l7/6l7q | 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: 17012.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus yayanosii (strain CH1 / JCM 16557) (archaea) Strain: CH1 / JCM 16557 / Gene: PYCH_01220 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8AFT0 |
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#2: 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: 53.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris (pH 8.5), 0.05M Magnesium sulfate, 1.8M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97943 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.16→23.956 Å / Num. obs: 51395 / % possible obs: 85.65 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.06 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Χ2: 1.8 / Net I/σ(I): 24.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.16→23.956 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.41 / Phase error: 17.83 / Stereochemistry target values: ML
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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 max: 39.64 Å2 / Biso mean: 16.4946 Å2 / Biso min: 7.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.16→23.956 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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