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Yorodumi- PDB-8u94: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u94 | |||||||||
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Title | Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (ADP Bound) | |||||||||
Components | Dephospho-CoA kinase | |||||||||
Keywords | TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | Function and homology information dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Klebsiella aerogenes KCTC 2190 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (ADP Bound) Authors: Seibold, S. / Lovell, S. / Liu, L. / Battaile, K.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u94.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u94.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 8u94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u94_validation.pdf.gz | 783 KB | Display | wwPDB validaton report |
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Full document | 8u94_full_validation.pdf.gz | 783.8 KB | Display | |
Data in XML | 8u94_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 8u94_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/8u94 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/8u94 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23850.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: coaE, EAE_11320 / Plasmid: KlaeA.00139.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FR62, dephospho-CoA kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MPD / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus E4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM ...Details: Morpheus E4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. 2 hour soak in 20mM ADP in crystallant. Plate: SS-Clover-3/17/23 H7/8, Puck: PSL-0112, Cryo: Direct' |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 28, 2023 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→49.02 Å / Num. obs: 39276 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.015 / Rrim(I) all: 0.041 / Χ2: 1 / Net I/σ(I): 21.2 / Num. measured all: 268372 |
Reflection shell | Resolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.921 / Num. measured all: 13233 / Num. unique obs: 1924 / CC1/2: 0.811 / Rpim(I) all: 0.376 / Rrim(I) all: 0.996 / Χ2: 0.95 / Net I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→24.04 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→24.04 Å
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Refine LS restraints |
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LS refinement shell |
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