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Yorodumi- PDB-8dv0: Crystal Structure of a Dephospho-CoA kinase from Rickettsia felis -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dv0 | ||||||
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Title | Crystal Structure of a Dephospho-CoA kinase from Rickettsia felis | ||||||
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 | Rickettsia felis URRWXCal2 (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, 1items
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Citation | Journal: to be published Title: Crystal Structure of a Dephospho-CoA kinase from Rickettsia felis Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / 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 | 8dv0.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dv0.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 8dv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dv0_validation.pdf.gz | 448.3 KB | Display | wwPDB validaton report |
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Full document | 8dv0_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 8dv0_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 8dv0_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/8dv0 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/8dv0 | HTTPS FTP |
-Related structure data
Related structure data | 4i1uS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23138.959 Da / Num. of mol.: 1 / Fragment: RifeA.01444.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia felis URRWXCal2 (bacteria) / Strain: ATCC VR-1525 / URRWXCal2 / Gene: coaE, RF_0177 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4UN30, dephospho-CoA kinase | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Wizard 3/4 D11 (307537d11): 100 mM MES/NaOH pH6.5, 200 mM Ammonium sulfate, 30% (w/v) PEG 5000 MME: RifeA.01444.a.B1.PW308220 @ 26.35 mg/mL: dephosphocoenzyme A @ 6.6mM (does not appear in ...Details: Wizard 3/4 D11 (307537d11): 100 mM MES/NaOH pH6.5, 200 mM Ammonium sulfate, 30% (w/v) PEG 5000 MME: RifeA.01444.a.B1.PW308220 @ 26.35 mg/mL: dephosphocoenzyme A @ 6.6mM (does not appear in structure): cryoprotected in reservoir supplemented with 15% ethylene glycol: puck/pin id: psd0-3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 15, 2020 / Details: Beryllium Lenses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.4→30.6 Å / Num. obs: 35777 / % possible obs: 95 % / Redundancy: 3.957 % / Biso Wilson estimate: 17.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.032 / Χ2: 0.949 / Net I/σ(I): 23.76 / Num. measured all: 141563 / Scaling rejects: 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I1U Resolution: 1.4→30.6 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.3 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.18 Å2 / Biso mean: 25.0737 Å2 / Biso min: 11.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→30.6 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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