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Yorodumi- PDB-4fl4: Scaffoldin conformation and dynamics revealed by a ternary comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fl4 | |||||||||
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Title | Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome | |||||||||
Components |
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Keywords | PROTEIN BINDING / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / cohesin / dockerin / X module / cell surface / hydrolase | |||||||||
Function / homology | Function and homology information S-layer / cellulase / cellulase activity / cellulose catabolic process / 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 / Resolution: 2.8 Å | |||||||||
Authors | Currie, M.A. / Adams, J.J. / Faucher, F. / Bayer, E.A. / Jia, Z. / Smith, S.P. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Scaffoldin Conformation and Dynamics Revealed by a Ternary Complex from the Clostridium thermocellum Cellulosome. Authors: Currie, M.A. / Adams, J.J. / Faucher, F. / Bayer, E.A. / Jia, Z. / Smith, S.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fl4.cif.gz | 421.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fl4.ent.gz | 338.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/4fl4 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/4fl4 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 3 types, 12 molecules ADGJBEHKCFIL
#1: Protein | Mass: 9948.213 Da / Num. of mol.: 4 / Fragment: type I dockerin (UNP residues 584-649) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cther_2220 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D1NID1, UniProt: A3DDN1*PLUS #2: Protein | Mass: 20550.199 Da / Num. of mol.: 4 / Fragment: type II cohesin (UNP residues 27-200) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: sdbA / Production host: Escherichia coli (E. coli) / References: UniProt: P71143 #3: Protein | Mass: 34659.938 Da / Num. of mol.: 4 Fragment: type I cohesin, X module, type II dockerin (UNP residues 9-320) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: ClothDRAFT_2952 / Production host: Escherichia coli (E. coli) / References: UniProt: C7HJU1, UniProt: Q46453*PLUS |
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-Non-polymers , 3 types, 117 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-SO4 / #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: 4.08 Å3/Da / Density % sol: 69.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 1.3-1.5 M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97927 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2009 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 105418 / Num. obs: 104697 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 73.99 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22.27 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.92 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10408 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.947 Å / SU ML: 0.76 / σ(F): 1.99 / Phase error: 25.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.818 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.947 Å
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Refine LS restraints |
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LS refinement shell |
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