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Yorodumi- PDB-2pc9: Crystal Structure Of ATP-Dependent Phosphoenolpyruvate Carboxykin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pc9 | ||||||
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Title | Crystal Structure Of ATP-Dependent Phosphoenolpyruvate Carboxykinase From Thermus thermophilus HB8 | ||||||
Components | Phosphoenolpyruvate carboxykinase [ATP] | ||||||
Keywords | LYASE / Phosphoenolpyruvate Carboxykinase / adenosine triphosphate / Thermus thermophilus HB8 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure Of ATP-Dependent Phosphoenolpyruvate Carboxykinase From Thermus thermophilus HB8 Authors: Sugahara, M. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pc9.cif.gz | 427.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pc9.ent.gz | 348.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pc9_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2pc9_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2pc9_validation.xml.gz | 84.2 KB | Display | |
Data in CIF | 2pc9_validation.cif.gz | 116.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/2pc9 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/2pc9 | HTTPS FTP |
-Related structure data
Related structure data | 1xkvS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 59387.191 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5SLL5, phosphoenolpyruvate carboxykinase (ATP) #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-ATP / #5: 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: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 295 K / Method: oil-micro batch / pH: 8.4 Details: 2.2M sodium phosphate, 5mM ATP, pH 8.4, oil-micro batch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 13, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 99306 / Num. obs: 99306 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.078 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.5 / Num. unique all: 9758 / Rsym value: 0.548 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XKV Resolution: 2.4→39.91 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→39.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.016
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