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Yorodumi- PDB-2bmu: UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bmu | ||||||
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Title | UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE UMP AND ITS SUBSTRATE ANALOG AMPPNP | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / UMP KINASE / AMINO ACID KINASE / PHOSPHORYL GROUP TRANSFER / PYRIMIDINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | PYROCOCCUS FURIOSUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Marco-Marin, C. / Gil-Ortiz, F. / Rubio, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The Crystal Structure of Pyrococcus Furiosus Ump Kinase Provides Insight Into Catalysis and Regulation in Microbial Pyrimidine Nucleotide Biosynthesis. Authors: Marco-Marin, C. / Gil-Ortiz, F. / 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 | 2bmu.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bmu.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/2bmu ftp://data.pdbj.org/pub/pdb/validation_reports/bm/2bmu | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.30291, -0.83757, 0.45466), Vector: |
-Components
#1: Protein | Mass: 24784.244 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PUKPFU / 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: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Compound details | FUNCTION: CATALYSATO | |
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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: 2.42 Å3/Da / Density % sol: 48.85 % |
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Crystal grow | pH: 8 / Details: 3.5 M SODIUM FORMATE, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96865 |
Detector | Type: MAR-USA, INC / 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: 0.96865 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→19.67 Å / Num. obs: 16529 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED SEMET PHASED MODEL Resolution: 2.55→19.67 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 4898792.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.9035 Å2 / ksol: 0.381603 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→19.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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