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Yorodumi- PDB-2hhg: Structure of Protein of Unknown Function RPA3614, Possible Tyrosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hhg | ||||||
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Title | Structure of Protein of Unknown Function RPA3614, Possible Tyrosine Phosphatase, from Rhodopseudomonas palustris CGA009 | ||||||
Components | Hypothetical protein RPA3614Hypothesis | ||||||
Keywords | Structural genomics / unknown function / MCSG / hypothetical protein / Rohopseudomonas palustris / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å | ||||||
Authors | Binkowski, T.A. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be published Title: Hypothetical protein RPA3614 from Rhodopseudomonas palustris CGA009 Authors: Binkowski, T.A. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hhg.cif.gz | 39.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hhg.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/2hhg ftp://data.pdbj.org/pub/pdb/validation_reports/hh/2hhg | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15243.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA3614 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N3S9 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-NA / |
#4: 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: 1.88 Å3/Da / Density % sol: 34.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.4M Na Citrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 10, 2006 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 33695 / Num. obs: 32294 / % possible obs: 95.84 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.2→1.24 Å / % possible all: 28.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.2→40.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.575 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.271 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→40.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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