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Yorodumi- PDB-4v1r: Structure of a selenomethionine derivative of the GH76 alpha- man... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v1r | ||||||
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Title | Structure of a selenomethionine derivative of the GH76 alpha- mannanase BT2949 Bacteroides thetaiotaomicron | ||||||
Components | ALPHA-1,6-MANNANASE | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / GH76 / CAZY / BACTEROIDES / POLYSACCHARIDE UTILISATION / ENZYME-CARBOHYDRATE INTERACTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Thompson, A.J. / Cuskin, F. / Spears, R.J. / Dabin, J. / Turkenburg, J.P. / Gilbert, H.J. / Davies, G.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structure of the Gh76 Alpha-Mannanase Homolog, Bt2949, from the Gut Symbiont Bacteroides Thetaiotaomicron Authors: Thompson, A.J. / Cuskin, F. / Spears, R.J. / Dabin, J. / Turkenburg, J.P. / Gilbert, H.J. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v1r.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v1r.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 4v1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v1r ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v1r | HTTPS FTP |
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-Related 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.00015, 0.00036), Vector: |
-Components
#1: Protein | Mass: 45769.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q8A3K5, mannan endo-1,6-alpha-mannosidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.44 Å3/Da / Density % sol: 64.29 % / Description: NONE |
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Crystal grow | pH: 7.2 / Details: 1.5 M AMMONIUM TARTRATE PH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97926 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.5 Å / Num. obs: 115956 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 7.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.8→126.16 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.701 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / 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 mean: 22.303 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→126.16 Å
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Refine LS restraints |
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