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Yorodumi- PDB-3oea: Crystal structure of the Q121E mutants of C.polysaccharolyticus C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oea | |||||||||
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Title | Crystal structure of the Q121E mutants of C.polysaccharolyticus CBM16-1 bound to cellopentaose | |||||||||
Components | S-layer associated multidomain endoglucanase | |||||||||
Keywords | HYDROLASE / Carbohydrate Binding Domain / Cellopentaose | |||||||||
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: 1.35 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 | 3oea.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oea.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 3oea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/3oea ftp://data.pdbj.org/pub/pdb/validation_reports/oe/3oea | HTTPS FTP |
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-Related structure data
Related structure data | 3oebC 2zexS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 16050.784 Da / Num. of mol.: 2 / 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 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: 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: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 30% PEG 3350, 100 mM Tris-HCl, 200 mM MgCl2, pH 8.3, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.35→25 Å / Num. all: 54672 / Num. obs: 54672 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 45.9 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 9.4 / Num. unique all: 2632 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2ZEX Resolution: 1.35→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.909 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R Free: 0.068 / 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: 14.207 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.386 Å / Total num. of bins used: 20
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