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- PDB-7d6a: Crystal structure of Oryza sativa Os4BGlu18 monolignol beta-gluco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d6a | |||||||||
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Title | Crystal structure of Oryza sativa Os4BGlu18 monolignol beta-glucosidase | |||||||||
![]() | Beta-glucosidase 18 | |||||||||
![]() | HYDROLASE / monolignol beta-glucosidase / Os4BGlu18 | |||||||||
Function / homology | ![]() coniferin metabolic process / coniferin beta-glucosidase activity / glycoside metabolic process / beta-D-fucosidase activity / scopolin beta-glucosidase activity / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Baiya, S. / Pengthaisong, S. / Ketudat Cairns, J.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of rice Os4BGlu18 monolignol beta-glucosidase. Authors: Baiya, S. / Pengthaisong, S. / Kitjaruwankul, S. / Ketudat Cairns, J.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.3 KB | Display | ![]() |
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PDB format | ![]() | 175.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.3 MB | Display | |
Data in XML | ![]() | 42.4 KB | Display | |
Data in CIF | ![]() | 64.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d6bC ![]() 2rglS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 domain:
NCS domain segments:
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Components
#1: Protein | Mass: 55331.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: BGLU18, Os04g0513900, LOC_Os04g43410, OSJNBa0004N05.26, OSJNBb0070J16.3 Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.09 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 19% PEG 3350, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288 K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 96808 / % possible obs: 96 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Num. unique obs: 9639 / CC1/2: 0.841 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RGL Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.867 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 58.2 Å2 / Biso mean: 18.725 Å2 / Biso min: 10.44 Å2
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Refinement step | Cycle: final / Resolution: 1.7→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7293 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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