+Open data
-Basic information
Entry | Database: PDB / ID: 2bne | ||||||
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Title | The structure of E. coli UMP kinase in complex with UMP | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / PYRIMIDINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleotide biosynthetic process / UDP biosynthetic process / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Briozzo, P. / Evrin, C. / Meyer, P. / Assairi, L. / Joly, N. / Barzu, O. / Gilles, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structure of Escherichia Coli Ump Kinase Differs from that of Other Nucleoside Monophosphate Kinases and Sheds New Light on Enzyme Regulation. Authors: Briozzo, P. / Evrin, C. / Meyer, P. / Assairi, L. / Joly, N. / Barzu, O. / Gilles, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bne.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bne.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bne ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bne | HTTPS FTP |
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-Related structure data
Related structure data | 2bndSC 2bnfC 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
#1: Protein | Mass: 25999.277 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P29464, UniProt: P0A7E9*PLUS, EC: 2.7.4.4 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: 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: 2.17 Å3/Da / Density % sol: 43 % |
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Crystal grow | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 19016 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11 |
Reflection shell | Highest resolution: 2.3 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BND Resolution: 2.3→25 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.8104 Å2 / ksol: 0.361948 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Xplor file |
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