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Yorodumi- PDB-6ckg: D-glycerate 3-kinase from Cryptococcus neoformans var. grubii ser... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ckg | ||||||
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Title | D-glycerate 3-kinase from Cryptococcus neoformans var. grubii serotype A (H99 / ATCC 208821 / CBS 10515 / FGSC 9487) | ||||||
Components | D-glycerate 3-kinase | ||||||
Keywords | TRANSFERASE / Cryptococcus neoformans / D-glycerate 3-kinase / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | kinase activity / P-loop containing nucleoside triphosphate hydrolase / D-glycerate 3-kinase Function and homology information | ||||||
Biological species | Cryptococcus neoformans var. grubii serotype A (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Horanyi, P.S. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: D-glycerate 3-kinase from Cryptococcus neoformans var. grubii serotype A (H99 / ATCC 208821 / CBS 10515 / FGSC 9487) Authors: Horanyi, P.S. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ckg.cif.gz | 257.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ckg.ent.gz | 205.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ckg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/6ckg ftp://data.pdbj.org/pub/pdb/validation_reports/ck/6ckg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37256.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_07779 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: J9VS00, glycerate 3-kinase #2: Chemical | ChemComp-EDO / #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: 2.6 Å3/Da / Density % sol: 52.75 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.4 uL 20 mg/mL JCSG+ B4, CrneC.19325.a.B1.PW38244 + 0.4 uL 0.1 M HEPES, pH 7.5, 10% w/v PEG8000, 8% v/v ethylene glycol, cryoprotectant: 20% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 26, 2017 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 53013 / % possible obs: 99.6 % / Redundancy: 6.1 % / Net I/σ(I): 15.78 |
Reflection shell | Resolution: 2→2.05 Å |
-Processing
Software |
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Refinement | Resolution: 2→38.52 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.52 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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