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Yorodumi- PDB-8sbo: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sbo | |||||||||
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Title | Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (P21 Form 2) | |||||||||
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 / 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 (P21 Form 2) Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Seibold, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sbo.cif.gz | 180 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sbo.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 8sbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sbo_validation.pdf.gz | 445.9 KB | Display | wwPDB validaton report |
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Full document | 8sbo_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 8sbo_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 8sbo_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/8sbo ftp://data.pdbj.org/pub/pdb/validation_reports/sb/8sbo | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23850.084 Da / Num. of mol.: 2 / Mutation: G2T, V127I 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 #2: Chemical | #3: Chemical | #4: 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: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus H4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine ...Details: Morpheus H4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. Plate: 13153, well H4 drop 1, Puck: PSL-1416, 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: Feb 14, 2022 |
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→63.81 Å / Num. obs: 77530 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.017 / Rrim(I) all: 0.047 / Χ2: 0.97 / Net I/σ(I): 16.2 / Num. measured all: 529323 |
Reflection shell | Resolution: 1.4→1.44 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.121 / Num. measured all: 38647 / Num. unique obs: 5715 / CC1/2: 0.774 / Rpim(I) all: 0.461 / Rrim(I) all: 1.214 / Χ2: 0.98 / Net I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→21.17 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.59 / 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→21.17 Å
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Refine LS restraints |
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LS refinement shell |
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