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Yorodumi- PDB-2vq4: Carbohydrate-binding of the starch binding domain of Rhizopus ory... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vq4 | ||||||
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Title | Carbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose | ||||||
Components | GLUCOAMYLASE A | ||||||
Keywords | HYDROLASE / RHIZOPUS ORYZAE GLUCOAMYLASE / CARBOHYDRATE BINDING / STARCH BINDING DOMAIN | ||||||
Function / homology | Function and homology information polysaccharide metabolic process / glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity Similarity search - Function | ||||||
Biological species | RHIZOPUS ORYZAE (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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. / Chou, W. / Liu, Y.-Y. / Yeh, Y. / Chang, F. / Lin, S. / Qiu, Z. / Sun, Y.-J. | ||||||
History |
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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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vq4.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vq4.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vq4 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vq4 | HTTPS FTP |
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-Related structure data
Related structure data | 2v8lSC 2v8mC S: Starting model for refinement C: citing same article (ref.) |
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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 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ILE 53 IS A CLONING VARIANT FROM A LOCAL STRAIN OF R. ORYZAE Source: (gene. exp.) RHIZOPUS ORYZAE (fungus) / Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q2VC81, glucan 1,4-alpha-glucosidase | ||
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#2: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence 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: 1.81 Å3/Da / Density % sol: 0.32 % / Description: NONE |
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Crystal grow | Details: 25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9732 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9732 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→30 Å / Num. obs: 23978 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.7 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V8L Resolution: 1.25→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.288 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.053 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 6, 42, 99, AND 101 ARE DISORDERED ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES SER 8, GLN10, SER 19, THR37, SER 44, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 6, 42, 99, AND 101 ARE DISORDERED ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES SER 8, GLN10, SER 19, THR37, SER 44, SER57, GLU68, AND SER89. HENCE THEIR ALTERNATE INDICATORS ARE A AND B. THEY CONCERNED HAVE OCCUPANCY BETWEEN 0.0 AND 1.0 AND WERE REFINED AS DESCRIBED ABOVE. OCCUPANCY VALUES LOWER THAN 1. 0 APPEARED TO JUSTIFY BETTER THE ELECTRON DENSITY.
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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: 12.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→30 Å
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Refine LS restraints |
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