[English] 日本語
Yorodumi- PDB-6ybr: RT structure of Glucose Isomerase obtained at 1.20 A resolution f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ybr | ||||||
---|---|---|---|---|---|---|---|
Title | RT structure of Glucose Isomerase obtained at 1.20 A resolution from crystal grown in a Mylar microchip. | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / XYLOSE ISOMERASE | ||||||
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces rubiginosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Gavira, J.A. / Martinez-Rodriguez, S. | ||||||
Funding support | Spain, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips. Authors: Gavira, J.A. / Rodriguez-Ruiz, I. / Martinez-Rodriguez, S. / Basu, S. / Teychene, S. / McCarthy, A.A. / Mueller-Dieckman, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ybr.cif.gz | 228.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ybr.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ybr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/6ybr ftp://data.pdbj.org/pub/pdb/validation_reports/yb/6ybr | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ybfC 6ybiC 6yboC 6ybxC 6yc5C 4a8iS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % |
---|---|
Crystal grow | Temperature: 293.5 K / Method: counter-diffusion / pH: 7 / Details: 0.1 M MgCl2, 10% w/v PEG 1K, 0.1 M Hepes pH 7.0 |
-Data collection
Diffraction | Mean temperature: 293.5 K / Ambient temp details: Room Temperature / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2017 Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→46.99 Å / Num. obs: 149874 / % possible obs: 99.95 % / Redundancy: 8.86 % / Biso Wilson estimate: 16.95 Å2 / CC1/2: 0.994 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.2→1.24 Å / Num. unique obs: 14856 / CC1/2: 0.41 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A8I Resolution: 1.2→46.99 Å / SU ML: 0.1343 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.6927
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→46.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|