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Yorodumi- PDB-2d4w: Crystal structure of glycerol kinase from Cellulomonas sp. NT3060 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d4w | ||||||
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Title | Crystal structure of glycerol kinase from Cellulomonas sp. NT3060 | ||||||
Components | glycerol kinase | ||||||
Keywords | TRANSFERASE / Alpha and beta protein / Ribonuclease H-like motif / Actin-like ATPase domain | ||||||
Function / homology | ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | Cellulomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIROAS / Resolution: 2.3 Å | ||||||
Authors | Imada, K. / Tamura, T. / Namba, K. / Inagaki, K. | ||||||
Citation | Journal: To be Published Title: Structure of glycerol kinase from Cellulomonas sp. NT3060 Authors: Imada, K. / Tamura, T. / Inagaki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d4w.cif.gz | 207 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d4w.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d4w_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 2d4w_full_validation.pdf.gz | 479.1 KB | Display | |
Data in XML | 2d4w_validation.xml.gz | 42.1 KB | Display | |
Data in CIF | 2d4w_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d4w ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d4w | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assmbly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 55195.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulomonas sp. (bacteria) / Strain: NT3060 / Production host: Escherichia coli (E. coli) / References: glycerol kinase #2: Chemical | ChemComp-MPD / ( #3: 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: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 4.5 Details: 27-37% MPD, 0.1M citrate, pH 4.5, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.13 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 5, 2003 |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.13 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→55.9 Å / Num. all: 50338 / Num. obs: 49935 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.3→2.42 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIROAS / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.016 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.327 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.374 Å / Total num. of bins used: 16 /
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