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Yorodumi- PDB-2whj: Understanding how diverse mannanases recognise heterogeneous subs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2whj | ||||||
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Title | Understanding how diverse mannanases recognise heterogeneous substrates | ||||||
Components | BETA-MANNANASE | ||||||
Keywords | HYDROLASE / MANNANASE / GLYCOSIDE HYDROLASE | ||||||
Function / homology | Function and homology information beta-mannosidase activity / mannan endo-1,4-beta-mannosidase / glucan catabolic process / mannan endo-1,4-beta-mannosidase activity / carbohydrate metabolic process / membrane Similarity search - Function | ||||||
Biological species | BACILLUS AGARADHAERENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Tailford, L.E. / Ducros, V.M.A. / Flint, J.E. / Roberts, S.M. / Morland, C. / Zechel, D.L. / Smith, N. / Bjornvad, M.E. / Borchert, T.V. / Wilson, K.S. ...Tailford, L.E. / Ducros, V.M.A. / Flint, J.E. / Roberts, S.M. / Morland, C. / Zechel, D.L. / Smith, N. / Bjornvad, M.E. / Borchert, T.V. / Wilson, K.S. / Davies, G.J. / Gilbert, H.J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Understanding How Diverse -Mannanases Recognise Heterogeneous Substrates. Authors: Tailford, L.E. / Ducros, V.M.A. / Flint, J.E. / Roberts, S.M. / Morland, C. / Zechel, D.L. / Smith, N. / Bjornvad, M.E. / Borchert, T.V. / Wilson, K.S. / Davies, G.J. / Gilbert, H.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2whj.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2whj.ent.gz | 118.8 KB | Display | PDB format |
PDBx/mmJSON format | 2whj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/2whj ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2whj | HTTPS FTP |
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-Related structure data
Related structure data | 2whkC 2whlC 2whmC 1bqcS 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: 34242.168 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Strain: NCIMB 40482 / Production host: BACILLUS SUBTILIS (bacteria) References: UniProt: Q5YEX6, UniProt: G1K3N4*PLUS, mannan endo-1,4-beta-mannosidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | Details: 1.8M AMSO4, 0.1M NA-CITRATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→20 Å / Num. obs: 32878 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 42 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 6.8 / % possible all: 45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BQC Resolution: 1.78→95.35 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.821 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.101 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→95.35 Å
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Refine LS restraints |
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