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Yorodumi- PDB-6g1i: GH124 cellulase from Ruminiclostridium thermocellum in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g1i | |||||||||
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Title | GH124 cellulase from Ruminiclostridium thermocellum in complex with Mn and fructosylated cellopentaose | |||||||||
Components | Glycosyl HydrolaseGlycoside hydrolase | |||||||||
Keywords | HYDROLASE / Metal binding / 2-oxohistidine / cellulase | |||||||||
Function / homology | Function and homology information polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridium thermocellum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å | |||||||||
Authors | Urresti, S. / Davies, G.J. / Walton, P.H. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Structural studies of the unusual metal-ion site of the GH124 endoglucanase from Ruminiclostridium thermocellum. Authors: Urresti, S. / Cartmell, A. / Liu, F. / Walton, P.H. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g1i.cif.gz | 216.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g1i.ent.gz | 172.5 KB | Display | PDB format |
PDBx/mmJSON format | 6g1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/6g1i ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g1i | HTTPS FTP |
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-Related structure data
Related structure data | 6g1gC 2xqoS 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25347.975 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 131-350. Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria) Gene: Cthe_0435 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DCJ4 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | |
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-Non-polymers , 3 types, 465 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.01 Å3/Da / Density % sol: 38.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Tacsimate, PEG 3350, Manganese (II) acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→74.17 Å / Num. all: 1203487 / Num. obs: 215828 / % possible obs: 95.3 % / Redundancy: 5.6 % / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 0.99→1.01 Å / Redundancy: 2.3 % / Num. unique obs: 6811 / % possible all: 62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XQO Resolution: 0.99→53.59 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.802 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.953 Å2
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Refinement step | Cycle: 1 / Resolution: 0.99→53.59 Å
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Refine LS restraints |
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