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Yorodumi- PDB-2whm: Cellvibrio japonicus Man26A E121A and E320G double mutant in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2whm | |||||||||
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Title | Cellvibrio japonicus Man26A E121A and E320G double mutant in complex with mannobiose | |||||||||
Components | ENDO-1,4-BETA MANNANASE, MAN26A | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / MAN26 / GH-A CLAN / MANNANASE / GLYCOSIDASE | |||||||||
Function / homology | Function and homology information glucomannan metabolic process / galactomannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Durcos, V.M.A. / Davies, G.J. / Flint, J.E. / 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 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2whm.cif.gz | 181.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2whm.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 2whm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2whm_validation.pdf.gz | 852.1 KB | Display | wwPDB validaton report |
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Full document | 2whm_full_validation.pdf.gz | 854.1 KB | Display | |
Data in XML | 2whm_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 2whm_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/2whm ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2whm | HTTPS FTP |
-Related structure data
Related structure data | 2whjC 2whkC 2whlC 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 43486.352 Da / Num. of mol.: 1 / Fragment: RESIDUES 39-423 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: B3PBK3, UniProt: P49424*PLUS, mannan endo-1,4-beta-mannosidase |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 427 molecules
#3: Chemical | ChemComp-ZN / | ||
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#4: Chemical | ChemComp-NA / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | MANNOSE (MAN): FOUND AS PART OF A BETA 1-4 LINKED MNNOBIOSIDSequence details | ENZYME IS DOUBLE VARIANT E121A E320G | |
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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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 100MMTRIS PH7, 26% MEONOMETHYLETHER PEG550, 3MM ZNSO4, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 73813 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 53 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GW1 Resolution: 1.5→19.98 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.771 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.056 / 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: 18.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.98 Å
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Refine LS restraints |
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