+Open data
-Basic information
Entry | Database: PDB / ID: 7uwv | ||||||
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Title | CBM74 from Ruminococcus bromii Sas6 with maltodecaose | ||||||
Components | CBM74 | ||||||
Keywords | SUGAR BINDING PROTEIN / CBM74 / Sas6 / Ruminococcus bromii / starch binding protein / maltodecaose | ||||||
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: 1.7 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 | 7uwv.cif.gz | 226.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uwv.ent.gz | 178.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uwv_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7uwv_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7uwv_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 7uwv_validation.cif.gz | 42.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/7uwv ftp://data.pdbj.org/pub/pdb/validation_reports/uw/7uwv | HTTPS FTP |
-Related structure data
Related structure data | 7uwuSC 7uwwC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57526.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Gene: RBL236_00020 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N0UYM2 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Type: oligosaccharide / Mass: 1963.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 678 molecules
#4: Chemical | #5: Chemical | ChemComp-NA / | #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: 3.29 Å3/Da / Density % sol: 62.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% Tacsimate, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→80.04 Å / Num. obs: 84139 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.057 / Net I/σ(I): 17.2 / Num. measured all: 512902 / 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: 1.7→80.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.882 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 73 Å2 / Biso mean: 30.171 Å2 / Biso min: 17.82 Å2
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Refinement step | Cycle: final / Resolution: 1.7→80.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 38.9175 Å / Origin y: 41.2688 Å / Origin z: 43.5364 Å
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