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Yorodumi- PDB-2v4y: THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v4y | ||||||
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Title | THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERIC REGULATOR GTP | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / NUCLEOTIDE-BINDING / PYRIMIDINE BIOSYNTHESIS / ATP-BINDING / ALLOSTERIC ENZYME / GTP / KINASE / ALLOSTERY / NMP KINASE | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleotide biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Meyer, P. / Evrin, C. / Briozzo, P. / Joly, N. / Barzu, O. / Gilles, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural and Functional Characterization of Escherichia Coli Ump Kinase in Complex with its Allosteric Regulator GTP. Authors: Meyer, P. / Evrin, C. / Briozzo, P. / 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 | 2v4y.cif.gz | 278.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v4y.ent.gz | 225.2 KB | Display | PDB format |
PDBx/mmJSON format | 2v4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v4y_validation.pdf.gz | 4 MB | Display | wwPDB validaton report |
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Full document | 2v4y_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 2v4y_validation.xml.gz | 55.3 KB | Display | |
Data in CIF | 2v4y_validation.cif.gz | 70.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/2v4y ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v4y | HTTPS FTP |
-Related structure data
Related structure data | 2bnfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 25999.277 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PDIA17 / References: UniProt: P0A7E9, UMP kinase #2: Chemical | ChemComp-GTP / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 159 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 159 TO ASN ...ENGINEERED | Nonpolymer details | GUANOSINE-5'-TRIPHOSPHATE (GTP): IN A1243, B1243, C1243, D1243, E1243, F1243 ONLY THE PHOSPHATE ...GUANOSINE-5'-TRIPHOSPHA | |
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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: 2.18 Å3/Da / Density % sol: 43.5 % / Description: NONE |
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Crystal grow | Details: 43% PEG 400, 100 MM SODIUM ACETATE, PH 4.6, 22.5 MM GTP, 100 MM NACL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2826 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2826 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.15 Å / Num. obs: 34062 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.8→2.88 Å / Redundancy: 7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BNF Resolution: 2.8→49.038 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 24.01 / 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 / Bsol: 43.97 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→49.038 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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