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Yorodumi- PDB-4qlk: Crystal structure of rice BGlu1 E176Q/Y341A mutant complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qlk | |||||||||
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Title | Crystal structure of rice BGlu1 E176Q/Y341A mutant complexed with cellotetraose | |||||||||
Components | Beta-glucosidase 7 | |||||||||
Keywords | HYDROLASE / BETA-ALPHA-BARRELS / OLIGOSACCHARIDE BINDING / TRANSGLUCOSYLATION | |||||||||
Function / homology | Function and homology information amygdalin beta-glucosidase activity / prunasin beta-glucosidase activity / beta-L-arabinosidase activity / cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / beta-mannosidase activity / glucan endo-1,3-beta-D-glucosidase activity / scopolin beta-glucosidase activity / beta-glucosidase ...amygdalin beta-glucosidase activity / prunasin beta-glucosidase activity / beta-L-arabinosidase activity / cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / beta-mannosidase activity / glucan endo-1,3-beta-D-glucosidase activity / scopolin beta-glucosidase activity / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process / protein homodimerization activity / extracellular region Similarity search - Function | |||||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 1.83 Å | |||||||||
Authors | Pengthaisong, S. / Ketudat Cairns, J.R. | |||||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Effects of active site cleft residues on oligosaccharide binding, hydrolysis, and glycosynthase activities of rice BGlu1 and its mutants Authors: Pengthaisong, S. / Ketudat Cairns, J.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qlk.cif.gz | 222.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qlk.ent.gz | 174.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/4qlk ftp://data.pdbj.org/pub/pdb/validation_reports/ql/4qlk | HTTPS FTP |
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-Related structure data
Related structure data | 4qljC 4qllC 3f5i 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein / Sugars , 2 types, 5 molecules AB
#1: Protein | Mass: 54635.387 Da / Num. of mol.: 2 / Mutation: E176Q/Y341A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Strain: Orion Gene: BGLU1, BGLU7, LOC_Os03g49600, Os03g0703000, Os3BGlu7, OSJNBa0004L11.16 Plasmid: PET32A+ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: Q75I93, beta-glucosidase #2: Polysaccharide | |
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-Non-polymers , 4 types, 844 molecules
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THIS CONFLICT IS IN GENBANK DATABASE AAA84906. |
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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: 2.34 Å3/Da / Density % sol: 47.45 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 20% PEG MME 5000, 0.2M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→30 Å / Num. obs: 87554 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rsym value: 0.084 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 8189 / Rsym value: 0.465 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid body refinement Starting model: 3F5I 3f5i Resolution: 1.83→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.379 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→30 Å
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Refine LS restraints |
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