[English] 日本語
Yorodumi- PDB-2v8l: Carbohydrate-binding of the starch binding domain of Rhizopus ory... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v8l | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Carbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose | |||||||||
Components | GLUCOAMYLASE A | |||||||||
Keywords | HYDROLASE / CARBOHYDRATE BINDING | |||||||||
Function / homology | Function and homology information glucan 1,4-alpha-glucosidase / polysaccharide metabolic process / glucan 1,4-alpha-glucosidase activity / fungal-type vacuole / metal ion binding Similarity search - Function | |||||||||
Biological species | RHIZOPUS ORYZAE (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Tung, J.-Y. / Liu, Y.-Y. / Sun, Y.-J. | |||||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: Crystal Structures of the Starch-Binding Domain from Rhizopus Oryzae Glucoamylase Reveal a Polysaccharide-Binding Path. Authors: Tung, J.-Y. / Chang, M.D.-T. / Chou, W.-I. / Liu, Y.-Y. / Yeh, Y. / Chang, F. / Lin, S. / Qiu, Z. / Sun, Y.-J. | |||||||||
History |
| |||||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v8l.cif.gz | 39.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v8l.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v8l_validation.pdf.gz | 998.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2v8l_full_validation.pdf.gz | 998.2 KB | Display | |
Data in XML | 2v8l_validation.xml.gz | 8 KB | Display | |
Data in CIF | 2v8l_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/2v8l ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v8l | HTTPS FTP |
-Related structure data
Related structure data | 2v8mC 2vq4C 2djmS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11662.581 Da / Num. of mol.: 1 / Fragment: STARCH BINDING DOMAIN, RESIDUES 26-131 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHIZOPUS ORYZAE (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2VC81, UniProt: B7XC04*PLUS, glucan 1,4-alpha-glucosidase |
---|---|
#2: Polysaccharide | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Sequence details | ILE 53 IS A CLONING VARIANT FROM A LOCAL STRAIN OF R. ORYZAE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: PEG8K, ZINC ACETATE, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 273 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 12310 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.25 / % possible all: 94.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DJM Resolution: 1.8→21.36 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 42088.1 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.9675 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→21.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|