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Yorodumi- PDB-2ddm: Crystal Structure of Pyridoxal Kinase from the Escherichia coli P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ddm | ||||||
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Title | Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene at 2.1 A resolution | ||||||
Components | Pyridoxine kinase | ||||||
Keywords | TRANSFERASE / pyridoxal kinase / ribokinase / pyridoxal 5'-phosphate / vitamin B6 / phosphorylation | ||||||
Function / homology | Function and homology information thiamine salvage / hydroxymethylpyrimidine kinase activity / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / pyridoxal phosphate binding / magnesium ion binding / protein homodimerization activity / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Safo, M.K. / Musayev, F.N. / di Salvo, M.L. / Hunt, S. / Claude, J.B. / Schirch, V. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2006 Title: Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases. Authors: Safo, M.K. / Musayev, F.N. / di Salvo, M.L. / Hunt, S. / Claude, J.B. / Schirch, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ddm.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ddm.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ddm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ddm_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 2ddm_full_validation.pdf.gz | 467.2 KB | Display | |
Data in XML | 2ddm_validation.xml.gz | 27 KB | Display | |
Data in CIF | 2ddm_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/2ddm ftp://data.pdbj.org/pub/pdb/validation_reports/dd/2ddm | HTTPS FTP |
-Related structure data
Related structure data | 2ddoC 2ddwC 1jxhS 1lhpS 1td2S C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The asymmetric unit contains the functional dimer |
-Components
#1: Protein | Mass: 30876.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HMS 174(DE3) / Gene: pdxK / Plasmid: pET22(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174(DE3) / References: UniProt: P40191, pyridoxal kinase #2: Chemical | #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: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21% PEG 4000, 100mM Tris-HCl, 200mM Na acetate, 40mM MgSO4, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 12, 2004 / Details: mirrors |
Radiation | Monochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→61.6 Å / Num. obs: 31487 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4009 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TD2, 1LHP, 1JXH Resolution: 2.1→19.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 63955.46 / 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: 58.8001 Å2 / ksol: 0.345566 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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