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Yorodumi- PDB-3oeb: Crystal structure of the Q121E mutant of C.polysaccharolyticus CB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oeb | |||||||||
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Title | Crystal structure of the Q121E mutant of C.polysaccharolyticus CBM16-1 bound to mannopentaose | |||||||||
Components | S-layer associated multidomain endoglucanase | |||||||||
Keywords | HYDROLASE / Family 16 CBM-1 / Carbohydrate Binding Module / Mannopentaose | |||||||||
Function / homology | Function and homology information S-layer / : / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | |||||||||
Biological species | Caldanaerobius polysaccharolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Agarwal, V. / Nair, S.K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Mutational insights into the roles of amino acid residues in ligand binding for two closely related family 16 carbohydrate binding modules. Authors: Su, X. / Agarwal, V. / Dodd, D. / Bae, B. / Mackie, R.I. / Nair, S.K. / Cann, I.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oeb.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oeb.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/3oeb ftp://data.pdbj.org/pub/pdb/validation_reports/oe/3oeb | HTTPS FTP |
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-Related structure data
Related structure data | 3oeaC 2zeyS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15825.557 Da / Num. of mol.: 1 / Fragment: UNP residues 614-756 / Mutation: Q121E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobius polysaccharolyticus (bacteria) Gene: celA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZA17 | ||
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-CA / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M ammonium sulfate, 100 mM MES, pH 6.5, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.55→25 Å / Num. all: 29267 / Num. obs: 29267 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 41.4 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1392 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2ZEY Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.257 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.511 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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