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Yorodumi- PDB-2ji5: Structure of UMP kinase from Pyrococcus furiosus complexed with UTP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ji5 | ||||||
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Title | Structure of UMP kinase from Pyrococcus furiosus complexed with UTP | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / AMINO ACID KINASE / PHOSPHOTRANSPHERASE / ALLOSTERIC REGULATION / PYRIMIDINE METABOLISM / KINASE / UMP KINASE / URIDYLATE KINASE / PYRIMIDINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | PYROCOCCUS FURIOSUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Marco-Marin, C. / Rubio, V. | ||||||
Citation | Journal: To be Published Title: The Structure of Ump Kinase from Pyrococcus Furiosus Complexed with Utp Authors: Marco-Marin, C. / Rubio, V. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ji5.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ji5.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 2ji5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ji5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2ji5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2ji5_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 2ji5_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2ji5 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2ji5 | HTTPS FTP |
-Related structure data
Related structure data | 2bmuS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.44518, 0.84925, 0.28388), Vector: |
-Components
#1: Protein | Mass: 24764.836 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q8U122, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.4 Å3/Da / Density % sol: 47.9 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 3.5 M SODIUM FORMATE, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97946 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 3, 2004 / Details: TOROIDAL MIRRORS |
Radiation | Monochromator: SILICON (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→72.55 Å / Num. obs: 9813 / % possible obs: 100 % / Observed criterion σ(I): 1.6 / Redundancy: 9.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BMU Resolution: 2.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 1.6
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.58 Å / Total num. of bins used: 10 / % reflection obs: 100 % |