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Yorodumi- PDB-4zxo: The structure of a GH26 beta-mannanase from Bacteroides ovatus, B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zxo | ||||||
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Title | The structure of a GH26 beta-mannanase from Bacteroides ovatus, BoMan26A. | ||||||
Components | Glycosyl hydrolase family 26 | ||||||
Keywords | HYDROLASE / Mannanase / GH26 / CAZy | ||||||
Function / homology | Function and homology information substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / extracellular region Similarity search - Function | ||||||
Biological species | Bacteroides ovatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Bagenholm, V. / Aurelius, O. / Logan, D.T. / Bouraoui, H. / Stalbrand, H. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus: ENZYME SYNERGY AND CRYSTAL STRUCTURE OF A beta-MANNANASE. Authors: Bagenholm, V. / Reddy, S.K. / Bouraoui, H. / Morrill, J. / Kulcinskaja, E. / Bahr, C.M. / Aurelius, O. / Rogers, T. / Xiao, Y. / Logan, D.T. / Martens, E.C. / Koropatkin, N.M. / Stalbrand, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zxo.cif.gz | 161.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zxo.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zxo_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 4zxo_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 4zxo_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 4zxo_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/4zxo ftp://data.pdbj.org/pub/pdb/validation_reports/zx/4zxo | HTTPS FTP |
-Related structure data
Related structure data | 2vx4S 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: 40156.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Due to a 22 residue signal peptide that is not part of the construct, the numbering should start from 23. Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02092 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7LW88 |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM MES buffer, 0.1 M potassium thiocyanate, 30% (w/v) PEG monoethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.272 Å / Num. obs: 52731 / % possible obs: 99.76 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.06347 / Net I/σ(I): 18.24 |
Reflection shell | Resolution: 1.5→1.554 Å / Mean I/σ(I) obs: 2.53 / % possible all: 99.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2vx4 Resolution: 1.5→41.272 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 16.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→41.272 Å
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Refine LS restraints |
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LS refinement shell |
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