+Open data
-Basic information
Entry | Database: PDB / ID: 2va1 | ||||||
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Title | Crystal structure of UMP kinase from Ureaplasma parvum | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / UMPK / KINASE / URIDYLATE KINASE / PYRIMIDINE BIOSYNTHESIS / AMINO ACID KINASE FAMILY | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | UREAPLASMA PARVUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Egeblad-Welin, L. / Welin, M. / Wang, L. / Eriksson, S. | ||||||
Citation | Journal: FEBS J. / Year: 2007 Title: Structural and Functional Investigations of Ureaplasma Parvum Ump Kinase - a Potential Antibacterial Drug Target Authors: Egeblad-Welin, L. / Welin, M. / Wang, L. / Eriksson, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2va1.cif.gz | 268.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2va1.ent.gz | 218.2 KB | Display | PDB format |
PDBx/mmJSON format | 2va1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2va1_validation.pdf.gz | 410.4 KB | Display | wwPDB validaton report |
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Full document | 2va1_full_validation.pdf.gz | 423 KB | Display | |
Data in XML | 2va1_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 2va1_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2va1 ftp://data.pdbj.org/pub/pdb/validation_reports/va/2va1 | HTTPS FTP |
-Related structure data
Related structure data | 2a1fS 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: Ens-ID: 1 / Refine code: 2
NCS oper:
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-Components
#1: Protein | Mass: 28255.668 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) UREAPLASMA PARVUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9PPX6, UMP kinase, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor #2: Chemical | ChemComp-PO4 / #3: 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: 2.4 Å3/Da / Density % sol: 47.9 % / Description: NONE |
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Crystal grow | Details: 0.2 M AMMONIUM FLUORIDE, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33.42 Å / Num. obs: 48558 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A1F Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.868 / SU B: 11.9 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.122 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 167-175 DEPENDING ON SUBUNIT ARE DISORDERED, EXCEPT FOR SUBUNIT E.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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