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Yorodumi- PDB-2gaa: Crystal structure of YFH7 from Saccharomyces cerevisiae: a putati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gaa | ||||||
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Title | Crystal structure of YFH7 from Saccharomyces cerevisiae: a putative P-loop containing kinase with a circular permutation. | ||||||
Components | Hypothetical 39.9 kDa protein | ||||||
Keywords | UNKNOWN FUNCTION / YFR007w / YFH7 | ||||||
Function / homology | Function and homology information Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / kinase activity / phosphorylation / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Chaptal, V. / Morera, S. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Crystal structure and functional analysis identify the P-loop containing protein YFH7 of Saccharomyces cerevisiae as an ATP-dependent kinase. Authors: Gueguen-Chaignon, V. / Chaptal, V. / Lariviere, L. / Costa, N. / Lopes, P. / Morera, S. / Nessler, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gaa.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gaa.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/2gaa ftp://data.pdbj.org/pub/pdb/validation_reports/ga/2gaa | HTTPS FTP |
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-Related structure data
Related structure data | 2ga8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40996.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: P43591 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.07 Å3/Da / Density % sol: 40.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 5000MME ammonium sulfate, pH 6.5,VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 23990 / Num. obs: 23765 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rsym value: 0.059 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 2.5 % / Num. unique all: 3436 / Rsym value: 0.378 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2GA8 Resolution: 1.95→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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