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Yorodumi- PDB-2dpn: Crystal Structure of the glycerol kinase from Thermus thermophilus HB8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dpn | ||||||
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Title | Crystal Structure of the glycerol kinase from Thermus thermophilus HB8 | ||||||
Components | Glycerol kinase | ||||||
Keywords | TRANSFERASE / 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 glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol catabolic process / ATP binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Asada, Y. / Sugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites. Authors: Sugahara, M. / Asada, Y. / Morikawa, Y. / Kageyama, Y. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dpn.cif.gz | 202 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dpn.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/2dpn ftp://data.pdbj.org/pub/pdb/validation_reports/dp/2dpn | HTTPS FTP |
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-Related structure data
Related structure data | 1wmmC 2hd9C 2zbnC 1bu6S 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 dimer |
-Components
#1: Protein | Mass: 53405.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W24 #2: 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: 2.63 Å3/Da / Density % sol: 53.31 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.5 Details: ammonium sulfate, sodium cacodylate, PEG 8000, glycerol anhydrous, pH 6.5, 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: Mar 14, 2006 / Details: mirror |
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: 2.8→30 Å / Num. all: 28303 / Num. obs: 28303 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 53.354 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 4.07 / Num. unique all: 2766 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BU6 Resolution: 2.8→29.77 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.57 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.93 Å / Rfactor Rfree error: 0.026
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