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Yorodumi- PDB-2php: Crystal structure of the C-terminal domain of protein MJ0236 (Y23... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2php | ||||||
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Title | Crystal structure of the C-terminal domain of protein MJ0236 (Y236_METJA) | ||||||
Components | Uncharacterized protein MJ0236 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Chlorine ion / PSI-2 / 10417a / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information hydroxymethylpyrimidine kinase / phosphooxymethylpyrimidine kinase / hydroxymethylpyrimidine kinase activity / thiamine phosphate synthase / phosphomethylpyrimidine kinase activity / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å | ||||||
Authors | Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the C-terminal domain of protein MJ0236 (Y236_METJA) Authors: Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2php.cif.gz | 154.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2php.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 2php.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2php ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2php | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21859.711 Da / Num. of mol.: 4 / Fragment: Residues 240-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Species: Methanocaldococcus jannaschii / Strain: DSM 2661, JAL-1, JCM 10045, NBRC 100440 / Gene: MJ0236 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57688 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% PEG6000, 2.0M Sodium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2007 / Details: mirrors |
Radiation | Monochromator: Si (111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. all: 63779 / Num. obs: 63779 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.413 / Num. unique all: 5451 / % possible all: 83.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.03→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Displacement parameters | Biso mean: 38.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.09 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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