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Yorodumi- PDB-7cvm: Crystal structure of glucose isomerase by fixed-target serial syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cvm | ||||||
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Title | Crystal structure of glucose isomerase by fixed-target serial synchrotron crystallography (500 ms) | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / room temperature structure / serial crystallography / serial synchrotron crystallography | ||||||
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: 2 Å | ||||||
Authors | Nam, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Crystals / Year: 2020 Title: Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder Authors: Park, S.Y. / Choi, H. / Eo, C. / Cho, Y. / 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 | 7cvm.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cvm.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/7cvm ftp://data.pdbj.org/pub/pdb/validation_reports/cv/7cvm | HTTPS FTP |
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-Related structure data
Related structure data | 7cvjC 7cvkC 7cvlC 5y4iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1659492 / 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: 2.84 Å3/Da / Density % sol: 56.64 % |
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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: 298.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2→72.46 Å / Num. obs: 33589 / % possible obs: 100 % / Redundancy: 30.8 % / CC1/2: 0.7069 / CC star: 0.9101 / Net I/σ(I): 2.05 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 3282 / CC1/2: 0.5605 / CC star: 0.8475 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Sample dehydration prevention: Polyimide films / Sample holding: Nylon mesh |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y4I Resolution: 2→72.05 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / 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: 72.41 Å2 / Biso mean: 19.2822 Å2 / Biso min: 4.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→72.05 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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