[English] 日本語
Yorodumi- PDB-2ebs: Crystal Structure Anaalysis of Oligoxyloglucan reducing-end-speci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ebs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure Anaalysis of Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH) D465N Mutant Complexed with a Xyloglucan Heptasaccharide | |||||||||
Components | Oligoxyloglucan reducing end-specific cellobiohydrolase | |||||||||
Keywords | HYDROLASE / BETA-PROPELLER / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information oligoxyloglucan reducing-end-specific cellobiohydrolase / oligoxyloglucan reducing-end-specific cellobiohydrolase activity / xyloglucan metabolic process / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | Geotrichum sp. M128 (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Yaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Miyazaki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Structural Basis for the Exo-mode of Action in GH74 Oligoxyloglucan Reducing End-specific Cellobiohydrolase. Authors: Yaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Tsuda, S. / Mitsuishi, Y. / Miyazaki, K. #1: Journal: Structure / Year: 2004 Title: Tandem repeat of a seven-bladed beta-propeller domain in oligoxyloglucan reducing-end-specific cellobiohydrolase Authors: Yaoi, K. / Kondo, H. / Noro, N. / Suzuki, M. / Tsuda, S. / Mitsuishi, Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ebs.cif.gz | 324.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ebs.ent.gz | 258.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ebs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/2ebs ftp://data.pdbj.org/pub/pdb/validation_reports/eb/2ebs | HTTPS FTP |
---|
-Related structure data
Related structure data | 1sqjS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 84973.742 Da / Num. of mol.: 2 / Fragment: residues 1-789 / Mutation: D465N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geotrichum sp. M128 (yeast) / Plasmid: pET29a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplus(de3)rp References: UniProt: Q8J0D2, oligoxyloglucan reducing-end-specific cellobiohydrolase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.17 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 100mM MES pH5.2-5.3, 5-6% (w/v) PEG 3000, 40% (w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2004 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 72255 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 6.1 / % possible all: 82.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SQJ Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.525 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.347 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.134 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
|