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Yorodumi- PDB-6zq5: Crystal structure of Chaetomium thermophilum Glycerol Kinase in P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zq5 | |||||||||
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Title | Crystal structure of Chaetomium thermophilum Glycerol Kinase in P2221 space group | |||||||||
Components | Glycerol kinase-like protein | |||||||||
Keywords | TRANSFERASE / Kinase / Glycerol / Metabolism | |||||||||
Function / homology | Function and homology information glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol catabolic process / phosphorylation / ATP binding Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å | |||||||||
Authors | Wilk, P. / Wator, E. / Malecki, P. / Grudnik, P. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Int J Mol Sci / Year: 2020 Title: Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum . Authors: Wilk, P. / Kuska, K. / Wator, E. / Malecki, P.H. / Wos, K. / Tokarz, P. / Dubin, G. / Grudnik, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zq5.cif.gz | 574.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zq5.ent.gz | 477 KB | Display | PDB format |
PDBx/mmJSON format | 6zq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/6zq5 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/6zq5 | HTTPS FTP |
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-Related structure data
Related structure data | 6zq4C 6zq6C 6zq7C 6zq8C 2d4wS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 57067.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Gene: CTHT_0042250 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SAG9 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.125-0.3 M CaCl2; 16-19% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.14→46.71 Å / Num. obs: 61278 / % possible obs: 89.9 % / Redundancy: 6.118 % / Biso Wilson estimate: 47.968 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.13 / Χ2: 1.059 / Net I/σ(I): 11.59 / Num. measured all: 374918 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2d4w Resolution: 2.14→46.71 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 135.37 Å2 / Biso mean: 58.8501 Å2 / Biso min: 24.94 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→46.71 Å
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