+Open data
-Basic information
Entry | Database: PDB / ID: 2whk | ||||||
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Title | Structure of Bacillus subtilis mannanase man26 | ||||||
Components | MANNAN ENDO-1,4-BETA-MANNOSIDASE | ||||||
Keywords | HYDROLASE / SECRETED / CLAN GH-A / MANNANASE / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / GLYCOSIDASE / GLYCOSIDE HYDROLASE | ||||||
Function / homology | Function and homology information substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ducros, V.M.A. / Davies, G.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 | 2whk.cif.gz | 160.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2whk.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 2whk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/2whk ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2whk | HTTPS FTP |
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-Related structure data
Related structure data | 2whjC 2whlC 2whmC 1gw1S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38019.133 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Plasmid: PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O05512, mannan endo-1,4-beta-mannosidase |
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-Non-polymers , 5 types, 360 molecules
#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | #5: Chemical | ChemComp-ZN / | #6: 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 35% PEG8K, 0.2M NA ACETATE, 0.1M TRIS PH 7 TO 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9688 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9688 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 40383 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 44 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 7.1 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GW1 Resolution: 1.7→19.48 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.593 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.1 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.48 Å
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Refine LS restraints |
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