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Yorodumi- PDB-8j5h: Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j5h | ||||||
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Title | Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine | ||||||
Components | Deoxyadenosine/deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / Albomycin / biosynthesis | ||||||
Function / homology | deoxynucleoside kinase activity / Deoxynucleoside kinase domain / Deoxynucleoside kinase / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / NITRATE ION / : / Deoxyadenosine/deoxycytidine kinase Function and homology information | ||||||
Biological species | Streptomyces sp. ATCC 700974 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Ushimaru, R. / Mori, T. / Liu, H.-w. / Abe, I. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine Authors: Ushimaru, R. / Mori, T. / Liu, H.-w. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j5h.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j5h.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 8j5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j5h_validation.pdf.gz | 771.1 KB | Display | wwPDB validaton report |
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Full document | 8j5h_full_validation.pdf.gz | 772 KB | Display | |
Data in XML | 8j5h_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 8j5h_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/8j5h ftp://data.pdbj.org/pub/pdb/validation_reports/j5/8j5h | 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: 27404.893 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. ATCC 700974 (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A0A370RDE4 |
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#2: Chemical | ChemComp-TV0 / Mass: 275.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5S / Feature type: SUBJECT OF INVESTIGATION |
#3: Chemical | ChemComp-NO3 / |
#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: 2.08 Å3/Da / Density % sol: 40.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.03 M citrate, 0.07 M Bis-Tris propane, 28% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.22 Å / Num. obs: 45024 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 7 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2233 / CC1/2: 0.921 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→44.22 Å / SU ML: 0.1162 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.5866 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 15.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→44.22 Å
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Refine LS restraints |
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LS refinement shell |
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