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Yorodumi- PDB-4yhg: NATIVE BACTEROIDETES-AFFILIATED GH5 CELLULASE LINKED WITH A POLYS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yhg | |||||||||
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Title | NATIVE BACTEROIDETES-AFFILIATED GH5 CELLULASE LINKED WITH A POLYSACCHARIDE UTILIZATION LOCUS | |||||||||
Components | GH5 | |||||||||
Keywords | HYDROLASE / beta alpha barrel / glycoside hydrolase / metagenomics | |||||||||
Function / homology | Function and homology information organic substance metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | |||||||||
Biological species | Bacteroidetes bacterium AC2a (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Naas, A.E. / MacKenzie, A.K. / Dalhus, B. / Eijsink, V.G.H. / Pope, P.B. | |||||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus. Authors: Naas, A.E. / MacKenzie, A.K. / Dalhus, B. / Eijsink, V.G. / Pope, P.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yhg.cif.gz | 311.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yhg.ent.gz | 253.1 KB | Display | PDB format |
PDBx/mmJSON format | 4yhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/4yhg ftp://data.pdbj.org/pub/pdb/validation_reports/yh/4yhg | HTTPS FTP |
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-Related structure data
Related structure data | 4yheSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 9 - 397 / Label seq-ID: 1 - 389
NCS oper:
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-Components
#1: Protein | Mass: 43623.602 Da / Num. of mol.: 2 / Mutation: E172A Source method: isolated from a genetically manipulated source Details: Synthetic DNA Source: (gene. exp.) Bacteroidetes bacterium AC2a (bacteria) Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A076MPD7, cellulase #2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotriose | #3: 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: 2.46 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.2 M potassium nitrate, 20 % w/v PEG 3350, 5mM Cellotetraose |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→71.401 Å / Num. all: 34325 / Num. obs: 34325 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.116 / Rsym value: 0.105 / Net I/av σ(I): 5.405 / Net I/σ(I): 10.2 / Num. measured all: 180101 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YHE Resolution: 2.4→71.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.315 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.05 Å2 / Biso mean: 42.408 Å2 / Biso min: 20.35 Å2
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Refinement step | Cycle: final / Resolution: 2.4→71.4 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 5576 / Type: TIGHT THERMAL / Rms dev position: 3.11 Å / Weight position: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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