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Yorodumi- PDB-1woq: Crystal Structure of Inorganic Polyphosphate/ATP-Glucomannokinase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1woq | ||||||
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Title | Crystal Structure of Inorganic Polyphosphate/ATP-Glucomannokinase From Arthrobacter sp. strain KM At 1.8 A Resolution | ||||||
Components | Inorganic polyphosphate/ATP-glucomannokinase | ||||||
Keywords | TRANSFERASE / polyphosphate / glucomannokinase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Arthrobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Mukai, T. / Kawai, S. / Mori, S. / Mikami, B. / Murata, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structure of Bacterial Inorganic Polyphosphate/ATP-glucomannokinase: INSIGHTS INTO KINASE EVOLUTION Authors: Mukai, T. / Kawai, S. / Mori, S. / Mikami, B. / Murata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1woq.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1woq.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 1woq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/1woq ftp://data.pdbj.org/pub/pdb/validation_reports/wo/1woq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28031.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: KM / Plasmid: pET21b-gmk / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7WT42, EC: 2.7.1.63 #2: Sugar | #3: Chemical | ChemComp-PO4 / #4: 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: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | pH: 8 / Details: pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 50787 / % possible obs: 97.7 % / Redundancy: 5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.262 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→14.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2236352.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.7974 Å2 / ksol: 0.437477 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→14.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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