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Yorodumi- PDB-1ygg: Crystal structure of phosphoenolpyruvate carboxykinase from Actin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ygg | ||||||
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Title | Crystal structure of phosphoenolpyruvate carboxykinase from Actinobacillus succinogenes | ||||||
Components | phosphoenolpyruvate carboxykinase | ||||||
Keywords | LYASE / phosphoenolpyruvate carboxykinase | ||||||
Function / homology | Function and homology information phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Actinobacillus succinogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Leduc, Y.A. / Prasad, L. / Laivenieks, M. / Zeikus, J.G. / Delbaere, L.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif. Authors: Leduc, Y.A. / Prasad, L. / Laivenieks, M. / Zeikus, J.G. / Delbaere, L.T. | ||||||
History |
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Remark 999 | SEQUENCE Residues are numbered to match E. coli PCK. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ygg.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ygg.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ygg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/1ygg ftp://data.pdbj.org/pub/pdb/validation_reports/yg/1ygg | HTTPS FTP |
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-Related structure data
Related structure data | 1ylhC 1oenS 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: 61895.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinobacillus succinogenes (bacteria) / Gene: pckA / Plasmid: pAsPCK / Production host: Escherichia coli (E. coli) / Strain (production host): PB25 References: UniProt: Q6W6X5, UniProt: A6VKV4*PLUS, phosphoenolpyruvate carboxykinase (ATP) | ||||
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#2: Chemical | #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: 3.1 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 285 K / pH: 5.5 Details: ammonium sulphate, potassium sodium tartrate, sodium citrate, MES buffer, DTT, EDTA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9984 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 30, 2003 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9984 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 62780 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.433 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1OEN Resolution: 1.85→26.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1769536.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1183 Å2 / ksol: 0.390493 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→26.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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