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Yorodumi- PDB-4dh2: Crystal structure of Coh-OlpC(Cthe_0452)-Doc435(Cthe_0435) comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dh2 | ||||||
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Title | Crystal structure of Coh-OlpC(Cthe_0452)-Doc435(Cthe_0435) complex: A novel type I Cohesin-Dockerin complex from Clostridium thermocellum ATTC 27405 | ||||||
Components |
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Keywords | CELL ADHESION/PROTEIN BINDING / cellulosome / cohesin / dockerin / type I cohesin-dockerin / protein-protein interaction / cell adhesion / CELL ADHESION-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium thermocellum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Alves, V.D. / Carvalho, A.L. / Najmudin, S.H. / Bras, J. / Prates, J.A.M. / Fontes, C.M.G.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Novel Clostridium thermocellum Type I Cohesin-Dockerin Complexes Reveal a Single Binding Mode. Authors: Bras, J.L. / Alves, V.D. / Carvalho, A.L. / Najmudin, S. / Prates, J.A. / Ferreira, L.M. / Bolam, D.N. / Romao, M.J. / Gilbert, H.J. / Fontes, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dh2.cif.gz | 196.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dh2.ent.gz | 157.5 KB | Display | PDB format |
PDBx/mmJSON format | 4dh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dh2_validation.pdf.gz | 460.2 KB | Display | wwPDB validaton report |
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Full document | 4dh2_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | 4dh2_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4dh2_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/4dh2 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/4dh2 | HTTPS FTP |
-Related structure data
Related structure data | 3ul4C 2cclS 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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Unit cell |
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-Components
#1: Protein | Mass: 19063.643 Da / Num. of mol.: 2 / Fragment: unp residues 99-257 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_0452 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner cells / References: UniProt: A3DCL1 #2: Protein | Mass: 9482.773 Da / Num. of mol.: 2 / Fragment: unp residues 32-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_0435 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner cells / References: UniProt: A3DCJ4 #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CA / #5: 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: 2.81 Å3/Da / Density % sol: 56.27 % |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 2 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.745→78.6 Å / Num. obs: 66027 / % possible obs: 99.9 % / Redundancy: 14.9 % / Rsym value: 0.09 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.74→1.84 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.887 / % possible all: 99.6 |
-Phasing
Phasing | Method: molecular replacement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 65309 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CCL Resolution: 1.75→39.3 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.47 / σ(F): 1.34 / Phase error: 21.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.56 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→39.3 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.4374 Å / Origin y: 9.5578 Å / Origin z: -9.7545 Å
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Refinement TLS group | Selection details: all |