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Yorodumi- PDB-4nes: Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nes | ||||||
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Title | Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP | ||||||
Components | UDP-N-acetylglucosamine 2-epimerase | ||||||
Keywords | ISOMERASE / UDP-glycosyltransferase/glycogen phosphorylase fold / UDP-GlcNAc 2-epimerase | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.42 Å | ||||||
Authors | Chen, S.C. / Yang, C.S. / Huang, C.H. / Chen, Y. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Crystal structures of the archaeal UDP-GlcNAc 2-epimerase from Methanocaldococcus jannaschii reveal a conformational change induced by UDP-GlcNAc. Authors: Chen, S.C. / Huang, C.H. / Yang, C.S. / Liu, J.S. / Kuan, S.M. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nes.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nes.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 4nes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/4nes ftp://data.pdbj.org/pub/pdb/validation_reports/ne/4nes | 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
#1: Protein | Mass: 43138.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Gene: wecB, MJ1504 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q58899, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) |
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#2: Chemical | ChemComp-UD1 / |
#3: Chemical | ChemComp-UDP / |
#4: 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: 2.37 Å3/Da / Density % sol: 48.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.1 Details: 40mM Tris-propane, 60mM citric acid, 16% PEG 3350, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9638, 0.9789, 0.9791 | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2013 | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.42→30 Å / Num. obs: 74655 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | ||||||||||||
Reflection shell | Resolution: 1.42→1.47 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.362 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.42→25.001 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→25.001 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
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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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