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Yorodumi- PDB-2ism: Crystal structure of the putative oxidoreductase (glucose dehydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ism | ||||||
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Title | Crystal structure of the putative oxidoreductase (glucose dehydrogenase) (TTHA0570) from thermus theromophilus HB8 | ||||||
Components | Putative oxidoreductase | ||||||
Keywords | SUGAR BINDING PROTEIN / BL41XU SPRING-8 / bladed beta-propellor / glucose dehydrogenase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Ebihara, A. / Shinkai, A. / Nakagawa, N. / Shimizu, N. / Yamamoto, M. / Kuramitsu, S. ...Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Ebihara, A. / Shinkai, A. / Nakagawa, N. / Shimizu, N. / Yamamoto, M. / Kuramitsu, S. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Putative Oxidoreductase (Glucose Dehydrogenase) (TTHA0570) from Thermus Theromophilus HB8 Authors: Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Ebihara, A. / Shinkai, A. / Nakagawa, N. / Shimizu, N. / Yamamoto, M. / Kuramitsu, S. / Shiro, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ism.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ism.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ism.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ism_validation.pdf.gz | 445.6 KB | Display | wwPDB validaton report |
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Full document | 2ism_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 2ism_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 2ism_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2ism ftp://data.pdbj.org/pub/pdb/validation_reports/is/2ism | HTTPS FTP |
-Related structure data
Related structure data | 2g8sS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38880.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKS3 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 12% PEG6000, 0.1M NaCl, 0.1M Na Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2006 / Details: Rh Coated Bent KB mirrors |
Radiation | Monochromator: ROTATED-INCLINED DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 45627 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.078 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.309 / Num. unique all: 4548 / Rsym value: 0.32 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G8S Resolution: 1.9→36.61 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 543137.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.2468 Å2 / ksol: 0.378514 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→36.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
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Xplor file |
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