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Yorodumi- PDB-1yvy: Crystal structure of Anaerobiospirillum succiniciproducens phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yvy | ||||||
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Title | Crystal structure of Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase | ||||||
Components | Phosphoenolpyruvate carboxykinase [ATP] | ||||||
Keywords | LYASE / p-loop / domain movement / kinase / succinate | ||||||
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 | Anaerobiospirillum succiniciproducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Cotelesage, J.J. / Prasad, L. / Zeikus, J.G. / Laivenieks, M. / Delbaere, L.T. | ||||||
Citation | Journal: Int.J.Biochem.Cell Biol. / Year: 2005 Title: Crystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop. Authors: Cotelesage, J.J. / Prasad, L. / Zeikus, J.G. / Laivenieks, M. / Delbaere, L.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yvy.cif.gz | 203.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yvy.ent.gz | 160.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yvy_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 1yvy_full_validation.pdf.gz | 462.3 KB | Display | |
Data in XML | 1yvy_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 1yvy_validation.cif.gz | 54.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/1yvy ftp://data.pdbj.org/pub/pdb/validation_reports/yv/1yvy | HTTPS FTP |
-Related structure data
-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
#1: Protein | Mass: 58709.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaerobiospirillum succiniciproducens (bacteria) Gene: pckA / Plasmid: pProEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha References: UniProt: O09460, phosphoenolpyruvate carboxykinase (ATP) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PEG MME 5000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2004 Details: Diamond (111) double-crystal monochromator Bent cylindrical Si-mirror (Rh coating) |
Radiation | Monochromator: Diamond (111) double-crystal monochromator Bent cylindrical Si-mirror (Rh coating) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 43637 / Num. obs: 35963 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.067 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3980 / Rsym value: 0.394 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→10 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.35→10 Å
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Refine LS restraints |
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