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Yorodumi- PDB-6n54: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n54 | ||||||
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Title | Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine monophosphate | ||||||
Components | Uridine-cytidine kinase 2 | ||||||
Keywords | CYTOSOLIC PROTEIN / Uridine-cytidine kinase 2 / UCK2 / Kinase / Complex / Azide | ||||||
Function / homology | Function and homology information uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.424 Å | ||||||
Authors | Cuthbert, B.J. / Nainar, S. / Spitale, R.C. / Goulding, C.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Methods / Year: 2020 Title: An optimized chemical-genetic method for cell-specific metabolic labeling of RNA. Authors: Nainar, S. / Cuthbert, B.J. / Lim, N.M. / England, W.E. / Ke, K. / Sophal, K. / Quechol, R. / Mobley, D.L. / Goulding, C.W. / Spitale, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n54.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n54.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 6n54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n54_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6n54_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6n54_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 6n54_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/6n54 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/6n54 | HTTPS FTP |
-Related structure data
Related structure data | 6n53C 6n55C 1ueiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28520.283 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UCK2, UMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZX2, uridine/cytidine kinase |
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-Non-polymers , 5 types, 158 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: 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: 3.47 Å3/Da / Density % sol: 64.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na/K phosphate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 198 K / Ambient temp details: cryo / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 29839 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Rpim(I) all: 0.04 / Rrim(I) all: 0.105 / Rsym value: 0.097 / Χ2: 1.764 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 1456 / CC1/2: 0.724 / Rpim(I) all: 0.437 / Χ2: 0.589 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UEI Resolution: 2.424→46.583 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.17 / 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: 2.424→46.583 Å
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Refine LS restraints |
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LS refinement shell |
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