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Yorodumi- PDB-2yqs: Crystal structure of uridine-diphospho-N-acetylglucosamine pyroph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yqs | ||||||
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Title | Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the product-binding form | ||||||
Components | UDP-N-acetylglucosamine pyrophosphorylase | ||||||
Keywords | TRANSFERASE / Pyrophosphorylase / N-acetylglucosamine / Uridine-diphospho-N-acetylglucosamine / Candida albicans | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Miki, K. / Maruyama, D. / Nishitani, Y. / Nonaka, T. / Kita, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structure of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism Authors: Maruyama, D. / Nishitani, Y. / Nonaka, T. / Kita, A. / Fukami, T.A. / Mio, T. / Yamada-Okabe, H. / Yamada-Okabe, T. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yqs.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yqs.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yqs_validation.pdf.gz | 814.5 KB | Display | wwPDB validaton report |
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Full document | 2yqs_full_validation.pdf.gz | 818.9 KB | Display | |
Data in XML | 2yqs_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 2yqs_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/2yqs ftp://data.pdbj.org/pub/pdb/validation_reports/yq/2yqs | HTTPS FTP |
-Related structure data
Related structure data | 2yqcSC 2yqhC 2yqjC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54727.832 Da / Num. of mol.: 1 / Mutation: S216L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: O74933, UDP-N-acetylglucosamine diphosphorylase |
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-Non-polymers , 5 types, 218 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-UD1 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 6000, 0.1M ammonium sulfate, 15% glycerol, 0.01M uridine-N-acetylglucosamine, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 9, 2004 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 23766 / % possible obs: 96 % / Redundancy: 7.2 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.093 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 8.5 / Rsym value: 0.213 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YQC Resolution: 2.3→19.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2766022.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The intensity of the reflection used for the refinement is more than 0 sigma, but that of the unique reflections in the table of the statistics of the X-ray crystallography at the article is ...Details: The intensity of the reflection used for the refinement is more than 0 sigma, but that of the unique reflections in the table of the statistics of the X-ray crystallography at the article is more than 1 sigma. Therefore, the number of reflections in the refinement section is larger than that in the data collection.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.2005 Å2 / ksol: 0.417031 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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