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Yorodumi- PDB-4bfn: Crystal Structure of the Starch-Binding Domain from Rhizopus oryz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bfn | |||||||||
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Title | Crystal Structure of the Starch-Binding Domain from Rhizopus oryzae Glucoamylase in Complex with isomaltotetraose | |||||||||
Components | GLUCOAMYLASE | |||||||||
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 Similarity search - Function | |||||||||
Biological species | RHIZOPUS ORYZAE (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | |||||||||
Authors | Chu, C.H. / Li, K.M. / Lin, S.W. / Sun, Y.J. | |||||||||
Citation | Journal: Proteins / Year: 2014 Title: Crystal Structures of Starch Binding Domain from Rhizopus Oryzae Glucoamylase in Complex with Isomaltooligosaccharide: Insights Into Polysaccharide Binding Mechanism of Cbm21 Family. Authors: Chu, C. / Li, K. / Lin, S. / Chang, M.D. / Jiang, T. / Sun, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bfn.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bfn.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bfn_validation.pdf.gz | 747.7 KB | Display | wwPDB validaton report |
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Full document | 4bfn_full_validation.pdf.gz | 748.4 KB | Display | |
Data in XML | 4bfn_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 4bfn_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bfn ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bfn | HTTPS FTP |
-Related structure data
Related structure data | 4bfoC 2v8lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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, glucan 1,4-alpha-glucosidase | ||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Water | ChemComp-HOH / | ||
Nonpolymer details | ALPHA-D-GLUCOSE (GLC): EACH ALPHA-D-GLUCOSE IS CONNECTED BY ALPHA-1,6 GLYCOSIDICSequence details | ILE 53 IS A CLONING VARIANT FROM A LOCAL STRAIN OF R. ORYZAE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 35 % / Description: NONE |
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Crystal grow | Details: 0.1 M NA-CITRATE PH 5.6, 18% PEG4000 AND 0.2 M NH4-ACETATE |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. obs: 20968 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 9.42 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.44 |
Reflection shell | Resolution: 1.32→1.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.52 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V8L Resolution: 1.32→22.746 Å / SU ML: 0.19 / σ(F): 0.07 / Phase error: 18.79 / Stereochemistry target values: ML Details: ASN101 LIES BEYOND THE REASONABLE RANGE OF RAMACHANDRAN PLOT DUE TO ITS INTERACTION WITH THE SURROUNDING RESIDUES. THUS, ASN101 IS LIMITED IN A RIGID CONDITION.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.804 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→22.746 Å
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Refine LS restraints |
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LS refinement shell |
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