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Yorodumi- PDB-4ums: The crystal structure of the seventh ScaB type I cohesin from Pse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ums | ||||||
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Title | The crystal structure of the seventh ScaB type I cohesin from Pseudobacteroides cellulosolvens | ||||||
Components | CELLULOSOMAL ANCHORING SCAFFOLDIN B | ||||||
Keywords | STRUCTURAL PROTEIN / CELLULOSOME / COHESINS / DOCKERINS / TYPE I BINDING SCAFFOLDIN SCAB | ||||||
Function / homology | Function and homology information S-layer / polysaccharide catabolic process / hormone activity / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | BACTEROIDES CELLULOSOLVENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Cameron, K. / Alves, V.D. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Combined Crystal Structure of a Type-I Cohesin, Mutation and Affinity-Binding Studies Reveal Structural Determinants of Cohesin-Dockerin Specificity Authors: Cameron, K. / Alves, V.D. / Bayer, E.A. / Gilbert, H.J. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ums.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ums.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ums.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ums_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
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Full document | 4ums_full_validation.pdf.gz | 424.9 KB | Display | |
Data in XML | 4ums_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 4ums_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/4ums ftp://data.pdbj.org/pub/pdb/validation_reports/um/4ums | HTTPS FTP |
-Related structure data
Related structure data | 2cclS 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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Unit cell |
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-Components
#1: Protein | Mass: 16958.141 Da / Num. of mol.: 1 Fragment: SEVENTH COHESIN MODULE OF SCAB, RESIDUES 1039-1186 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES CELLULOSOLVENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: Q6A564 |
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#2: Water | ChemComp-HOH / |
Sequence details | HAS A C-TERMINAL HIS TAG. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.2 M SODIUM CHLORIDE AND 20 % W/V PEG 3350. 30% GLYCEROL ADDED AS CRYOPROTECTANT., pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93929 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93929 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→45.58 Å / Num. obs: 13249 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.3 / % possible all: 9.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CCL Resolution: 1.84→45.58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.037 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE LAST 2 HISTIDINES ARE DISORDERED. ISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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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 mean: 30.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→45.58 Å
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Refine LS restraints |
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