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Yorodumi- PDB-2cun: Crystal structure of Phosphoglycerate Kinase from Pyrococcus hori... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cun | ||||||
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Title | Crystal structure of Phosphoglycerate Kinase from Pyrococcus horikoshii OT3 | ||||||
Components | Phosphoglycerate kinase | ||||||
Keywords | TRANSFERASE / Phosphoglycerate kinase / Structural Genomics / TANPAKU 3000 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Phosphoglycerate Kinase from Pyrococcus horikoshii OT3 Authors: Mizutani, H. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cun.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cun.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 2cun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cun_validation.pdf.gz | 478 KB | Display | wwPDB validaton report |
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Full document | 2cun_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 2cun_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 2cun_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/2cun ftp://data.pdbj.org/pub/pdb/validation_reports/cu/2cun | HTTPS FTP |
-Related structure data
Related structure data | 1vpeS S: Starting model for refinement |
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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, chain A & B in asymmetric unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46470.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58965, phosphoglycerate kinase |
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-Non-polymers , 5 types, 380 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #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: 2.74 Å3/Da / Density % sol: 55.11 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.5 Details: PEG 6000, MPD, HEPES, pH 7.5, microbatch, 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 JUPITER 210 / Detector: CCD / Date: Oct 1, 2004 / Details: mirrors |
Radiation | Monochromator: Bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 58103 / Num. obs: 58103 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.054 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.27 / Num. unique all: 5810 / Rsym value: 0.256 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VPE Resolution: 2.1→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1594550.5 / 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: 54.0678 Å2 / ksol: 0.338601 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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