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Yorodumi- PDB-4c1s: Glycoside hydrolase family 76 (mannosidase) Bt3792 from Bacteroid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c1s | ||||||
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Title | Glycoside hydrolase family 76 (mannosidase) Bt3792 from Bacteroides thetaiotaomicron VPI-5482 | ||||||
Components | GLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE | ||||||
Keywords | HYDROLASE / GUT MICROBIOTA | ||||||
Function / homology | Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / catalytic activity / Mainly Alpha / Putative alpha-1,6-mannanase Function and homology information | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cuskin, F. / Lowe, E.C. / Zhu, Y. / Temple, M. / Thompson, A.J. / Cartmell, A. / Piens, K. / Bracke, D. / Vervecken, W. / Munoz-Munoz, J.L. ...Cuskin, F. / Lowe, E.C. / Zhu, Y. / Temple, M. / Thompson, A.J. / Cartmell, A. / Piens, K. / Bracke, D. / Vervecken, W. / Munoz-Munoz, J.L. / Suits, M.D.L. / Boraston, A.B. / Williams, S.J. / Davies, G.J. / Abbott, W.D. / Martens, E.C. / Gilbert, H.J. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Human Gut Bacteroidetes Can Utilize Yeast Mannan Through a Selfish Mechanism. Authors: Cuskin, F. / Lowe, E.C. / Temple, M.J. / Zhu, Y. / Cameron, E.A. / Pudlo, N.A. / Porter, N.T. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Hamilton, B.S. / Chen, R. / Tolbert, ...Authors: Cuskin, F. / Lowe, E.C. / Temple, M.J. / Zhu, Y. / Cameron, E.A. / Pudlo, N.A. / Porter, N.T. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Hamilton, B.S. / Chen, R. / Tolbert, T.J. / Piens, K. / Bracke, D. / Vervecken, W. / Hakki, Z. / Speciale, G. / Munoz-Munoz, J.L. / Day, A. / Pena, M.J. / Mclean, R. / Suits, M.D. / Boraston, A.B. / Atherly, T. / Ziemer, C.J. / Williams, S.J. / Davies, G.J. / Abbott, D.W. / Martens, E.C. / Gilbert, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c1s.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c1s.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 4c1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c1s_validation.pdf.gz | 464.1 KB | Display | wwPDB validaton report |
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Full document | 4c1s_full_validation.pdf.gz | 476.9 KB | Display | |
Data in XML | 4c1s_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 4c1s_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/4c1s ftp://data.pdbj.org/pub/pdb/validation_reports/c1/4c1s | HTTPS FTP |
-Related structure data
Related structure data | 4c1rC 4utfC 3k7xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43430.590 Da / Num. of mol.: 2 / Fragment: ENZYMATIC FRAGMENT, RESIDUES 155-525 Source method: isolated from a genetically manipulated source Details: BT3792 GENE FRAGMENT ENCODING RESIDUES 155- 514 Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria) Gene: BT3792 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8A174, mannan endo-1,6-alpha-mannosidase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 8 Details: BT3792 AT A 20 MG PER ML BUFFERED IN IN 25 MM TRIS-HCL (PH 8.0), 500 MM NACL, 2 MM DTT WITH A RESERVOIR SOLUTION CONSISTING OF 5% GLYCEROL (V/V), 24% (W PER V) POLYETHYLENE GLYCOL 2,000 ...Details: BT3792 AT A 20 MG PER ML BUFFERED IN IN 25 MM TRIS-HCL (PH 8.0), 500 MM NACL, 2 MM DTT WITH A RESERVOIR SOLUTION CONSISTING OF 5% GLYCEROL (V/V), 24% (W PER V) POLYETHYLENE GLYCOL 2,000 MONOMETHYL ETHER, 0.25 M SODIUM ACETATE, AND BIS-TRIS-HCL (PH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98005 |
Detector | Type: MARRESEARCH MX-300HE / Detector: CCD / Date: Sep 14, 2012 Details: COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT) |
Radiation | Monochromator: KOHZU DOUBLE CRYSTAL MONOCHROMATOR (DCM), FEATURING INDIRECTLY WATER- COOLED FIRST CRYSTAL AND FLAT, LONG SECOND CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98005 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48 Å / Num. obs: 52497 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3K7X Resolution: 2.1→48.03 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.911 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 24.111 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→48.03 Å
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Refine LS restraints |
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