[English] 日本語
Yorodumi- PDB-1v4v: Crystal Structure Of UDP-N-Acetylglucosamine 2-Epimerase From The... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v4v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of UDP-N-Acetylglucosamine 2-Epimerase From Thermus Thermophilus HB8 | ||||||
Components | UDP-N-Acetylglucosamine 2-Epimerase | ||||||
Keywords | ISOMERASE / UDP-GlcNAc / Two Domains / Homodimer / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bagautdinov, B. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: The Structure Of UDP-N-Acetylglucosamine 2-Epimerase From Thermus Thermophilus HB8 Authors: Bagautdinov, B. / Tahirov, T.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1v4v.cif.gz | 178.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1v4v.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 1v4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v4v_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1v4v_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | 1v4v_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 1v4v_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/1v4v ftp://data.pdbj.org/pub/pdb/validation_reports/v4/1v4v | HTTPS FTP |
-Related structure data
Related structure data | 1f6dS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 41402.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cap5P / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P83824, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) #2: Chemical | ChemComp-ACY / | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.64 % |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / pH: 8 Details: PEG 4000, Acetate, pH 8, MICROBATCH, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9787 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 5, 2003 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 81276 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.2 / Num. unique all: 20058 / % possible all: 88.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F6D Resolution: 1.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
|