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Yorodumi- PDB-7e03: Room temperature structure of glucose isomerase delivered in beef... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7000 | ||||||
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Title | Room temperature structure of glucose isomerase delivered in beef tallow by serial millisecond crystallography | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / serial crystallography / beef tallow / room temperature / glucose 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: 1.6 Å | ||||||
Authors | Nam, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Room temperature structure of glucose isomerase delivered in beef tallow by serial millisecond crystallography Authors: Nam, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e03.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e03.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 7e03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e03_validation.pdf.gz | 420.6 KB | Display | wwPDB validaton report |
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Full document | 7e03_full_validation.pdf.gz | 421 KB | Display | |
Data in XML | 7e03_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 7e03_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/7e03 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/7e03 | HTTPS FTP |
-Related structure data
Related structure data | 5y4iS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1844337 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-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 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.25 % |
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Crystal grow | Temperature: 293.5 K / Method: batch mode / pH: 7 / Details: Tris-HCl, Ammonium sulfate, Magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→72.46 Å / Num. obs: 64497 / % possible obs: 100 % / Redundancy: 250.9 % / CC1/2: 0.9656 / Net I/σ(I): 4.79 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 6368 / CC1/2: 0.5348 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y4I Resolution: 1.6→71.82 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.95 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.76 Å2 / Biso mean: 22.9293 Å2 / Biso min: 8.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→71.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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