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Yorodumi- PDB-5ujs: 2.45 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ujs | ||||||
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Title | 2.45 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Campylobacter jejuni. | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | HYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase. | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / cell cycle / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | Campylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Stam, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.45 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Campylobacter jejuni. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Stam, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ujs.cif.gz | 340.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ujs.ent.gz | 277.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ujs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/5ujs ftp://data.pdbj.org/pub/pdb/validation_reports/uj/5ujs | HTTPS FTP |
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-Related structure data
Related structure data | 5bq2S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: -1 - 417 / Label seq-ID: 23 - 441
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-Components
#1: Protein | Mass: 47982.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter) Strain: ATCC 700819 / NCTC 11168 / Gene: murA, Cj0858c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9PP65, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-CL / | #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: 2.14 Å3/Da / Density % sol: 42.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 7.7 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: PEG II (D1), 0.1M Sodium acetate, 0.1 HEPES (pH 7.5), 22% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2009 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 29963 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.045 / Rsym value: 0.075 / Χ2: 1.011 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1348 / CC1/2: 0.77 / Rrim(I) all: 0.34 / Rsym value: 0.538 / Χ2: 1 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BQ2 Resolution: 2.46→29.93 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 29.822 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 1.087 / ESU R Free: 0.335 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.486 Å2
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Refinement step | Cycle: 1 / Resolution: 2.46→29.93 Å
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Refine LS restraints |
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