+Open data
-Basic information
Entry | Database: PDB / ID: 3icp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of UDP-galactose 4-epimerase | ||||||
Components | NAD-dependent epimerase/dehydratase | ||||||
Keywords | ISOMERASE / Rossmann fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrobaculum calidifontis (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Sakuraba, H. / Kawai, T. / Yoneda, K. / Ohshima, T. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of UDP-galactose 4-epimerase Authors: Sakuraba, H. / Kawai, T. / Yoneda, K. / Ohshima, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3icp.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3icp.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 3icp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/3icp ftp://data.pdbj.org/pub/pdb/validation_reports/ic/3icp | HTTPS FTP |
---|
-Related structure data
Related structure data | 3eheS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 34396.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: JCM 11548 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3MUJ4 |
---|---|
#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.39 % |
---|---|
Crystal grow | Temperature: 293 K / Method: sitting drop / pH: 6.6 Details: 2-ethoxy ethanol, pH 6.6, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 6, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→71.429 Å / Num. all: 26825 / Num. obs: 26762 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.051 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 14 % / Mean I/σ(I) obs: 9.8 / Num. unique all: 2612 / Rsym value: 0.235 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EHE Resolution: 2.01→33.55 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2181189 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.938 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.1 Å2 / Biso mean: 25.205 Å2 / Biso min: 8.31 Å2
| ||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→33.55 Å
| ||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.01→2.14 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||
Xplor file |
|