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- PDB-3l8q: Structure analysis of the type II cohesin dyad from the adaptor S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l8q | ||||||
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Title | Structure analysis of the type II cohesin dyad from the adaptor ScaA scaffoldin of Acetivibrio cellulolyticus | ||||||
![]() | Cellulosomal scaffoldin adaptor protein B | ||||||
![]() | STRUCTURAL PROTEIN / PROTEIN BINDING / Dockerin-binding module / protein-protein interactions / linker segment / scaffoldin arrangement / beta sandwich / alpha helix / beta flaps | ||||||
Function / homology | ![]() polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Noach, I. / Frolow, F. / Bayer, E.A. | ||||||
![]() | ![]() Title: Modular Arrangement of a Cellulosomal Scaffoldin Subunit Revealed from the Crystal Structure of a Cohesin Dyad Authors: Noach, I. / Levy-Assaraf, M. / Lamed, R. / Shimon, L.J.W. / Frolow, F. / Bayer, E.A. #1: ![]() Title: Intermodular linker flexibility revealed from crystal structures of adjacent cellulosomal cohesins of Acetivibrio cellulolyticus Authors: Noach, I. / Frolow, F. / Alber, O. / Lamed, R. / Shimon, L.J.W. / Bayer, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 623.2 KB | Display | ![]() |
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PDB format | ![]() | 513 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zv9S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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
#1: Protein | Mass: 37897.426 Da / Num. of mol.: 4 / Fragment: Cohesin dyad, UNP residues 28-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-HEZ / | #5: Water | ChemComp-HOH / | Sequence details | THE DEPOSITORS SUSPECT THAT THE ORIGINAL SEQUENCING WAS MISTAKEN AT THIS POSITION. THEIR RESULTS ...THE DEPOSITORS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.51 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 0.15M citric acid pH 3.5, 16% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2007 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→30 Å / Num. obs: 192139 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 23.9 / Num. measured all: 707451 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8616 / Rsym value: 0.446 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZV9 Resolution: 1.57→29.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.799 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; THE FRIEDEL PAIRS WERE USED FOR phasing.
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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: 15.626 Å2
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Refine analyze | Luzzati coordinate error obs: 0.203 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→29.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.572→1.603 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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