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Yorodumi- PDB-3ek5: Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ek5 | ||||||
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Title | Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium | ||||||
Components | Uridylate kinase | ||||||
Keywords | TRANSFERASE / Xanthomonas campestris / UMPK crystal structure / unique GTP binding site / allosteric regulation / ATP-binding / Kinase / Nucleotide-binding / Pyrimidine biosynthesis | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Tu, J.-L. / Chin, K.-H. / Wang, A.H.-J. / Chou, S.-H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Unique GTP-Binding Pocket and Allostery of Uridylate Kinase from a Gram-Negative Phytopathogenic Bacterium Authors: Tu, J.-L. / Chin, K.-H. / Wang, A.H.-J. / Chou, S.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ek5.cif.gz | 290.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ek5.ent.gz | 234.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ek5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ek5_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 3ek5_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 3ek5_validation.xml.gz | 63.3 KB | Display | |
Data in CIF | 3ek5_validation.cif.gz | 86.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/3ek5 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/3ek5 | HTTPS FTP |
-Related structure data
Related structure data | 3ek6SC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 4
NCS ensembles :
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-Components
#1: Protein | Mass: 26057.082 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Strain: XC17 / Gene: pyrH, XCC1371 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59009, UMP kinase #2: Chemical | ChemComp-GTP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M Na Citrate, 19.5% PEG 3350, 0.05M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97315 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97315 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→86.39 Å / Num. all: 55638 / Num. obs: 55392 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Rsym value: 0.05 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 5 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5439 / Rsym value: 0.3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EK6 Resolution: 2.56→27.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 21.137 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.709 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that are not the terminal residues of the sequence. In all these instances the OXT was ...Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that are not the terminal residues of the sequence. In all these instances the OXT was changed to N of the next residue
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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: 55.136 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→27.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.56→2.606 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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