+Open data
-Basic information
Entry | Database: PDB / ID: 7uww | ||||||
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Title | Sas6 with alpha-cyclodextrin | ||||||
Components | Starch Adherence System protein 6 (Sas6) | ||||||
Keywords | SUGAR BINDING PROTEIN / CBM74 / CBM26 / carbohydrate-binding module / starch-binding protein | ||||||
Function / homology | Function and homology information cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | Ruminococcus bromii L2-63 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Photenhauer, A.L. / Koropatkin, N.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: The Ruminococcus bromii amylosome protein Sas6 binds single and double helical alpha-glucan structures in starch. Authors: Photenhauer, A.L. / Villafuerte-Vega, R.C. / Cerqueira, F.M. / Armbruster, K.M. / Marecek, F. / Chen, T. / Wawrzak, Z. / Hopkins, J.B. / Vander Kooi, C.W. / Janecek, S. / Ruotolo, B.T. / Koropatkin, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uww.cif.gz | 498.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uww.ent.gz | 409.6 KB | Display | PDB format |
PDBx/mmJSON format | 7uww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uww_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7uww_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7uww_validation.xml.gz | 61 KB | Display | |
Data in CIF | 7uww_validation.cif.gz | 94.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/7uww ftp://data.pdbj.org/pub/pdb/validation_reports/uw/7uww | HTTPS FTP |
-Related structure data
Related structure data | 7uwuSC 7uwvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 68911.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Gene: Sas6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: A0A2N0UYM2 #2: Polysaccharide | Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 1492 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SCN / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.24 Å3/Da / Density % sol: 44.98 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7 / Details: PEG 3350, Potassium thiocyanate, TEW |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 13, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.61→35 Å / Num. obs: 122358 / % possible obs: 77 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.025 / Rrim(I) all: 0.095 / Net I/σ(I): 16 / Num. measured all: 1690626 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7UWU Resolution: 1.61→34.995 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.22 Å2 / Biso mean: 23.7454 Å2 / Biso min: 5.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.61→34.995 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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