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Yorodumi- PDB-1xkv: Crystal Structure Of ATP-Dependent Phosphoenolpyruvate Carboxykin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xkv | |||||||||
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Title | Crystal Structure Of ATP-Dependent Phosphoenolpyruvate Carboxykinase From Thermus thermophilus HB8 | |||||||||
Components | ATP-dependent phosphoenolpyruvate carboxykinase | |||||||||
Keywords | LYASE / Phosphoenolpyruvate Carboxykinase / adenosine triphosphate / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | |||||||||
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: 2.2 Å | |||||||||
Authors | Sugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability. Authors: Sugahara, M. / Ohshima, N. / Ukita, Y. / 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 | 1xkv.cif.gz | 234.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xkv.ent.gz | 185 KB | Display | PDB format |
PDBx/mmJSON format | 1xkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xkv_validation.pdf.gz | 801.1 KB | Display | wwPDB validaton report |
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Full document | 1xkv_full_validation.pdf.gz | 814.7 KB | Display | |
Data in XML | 1xkv_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 1xkv_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/1xkv ftp://data.pdbj.org/pub/pdb/validation_reports/xk/1xkv | HTTPS FTP |
-Related structure data
Related structure data | 1j3bSC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological assembly is a dimer. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59387.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) References: UniProt: Q5SLL5, phosphoenolpyruvate carboxykinase (ATP) |
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-Non-polymers , 5 types, 749 molecules
#2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-ATP / | #5: Chemical | #6: 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: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.8 Details: potassium phosphate, sodium phosphate, ATP, pH 6.8, microbatch, temperature 291K |
-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: Feb 4, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 75829 / Num. obs: 75829 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.077 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4.1 / Num. unique all: 7470 / Rsym value: 0.497 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J3B Resolution: 2.2→38.93 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→38.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.014
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