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Yorodumi- PDB-6zj6: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zj6 | ||||||||||||||||||
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Title | Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with cyclohexylmethyl-Glc-1,3-isofagomine | ||||||||||||||||||
Components | Glycosyl hydrolase family 71 | ||||||||||||||||||
Keywords | HYDROLASE / mannosidase / retaining | ||||||||||||||||||
Function / homology | Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / alpha-mannosidase activity / membrane / ACETATE ION / alpha-D-glucopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / methylcyclohexane / Glycosyl hydrolase family 71 Function and homology information | ||||||||||||||||||
Biological species | Bacteroides xylanisolvens XB1A (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||||||||||||||
Authors | Thompson, A.J. / Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. ...Thompson, A.J. / Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J. | ||||||||||||||||||
Funding support | United Kingdom, Australia, 5items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target. Authors: Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zj6.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zj6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zj6_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6zj6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6zj6_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6zj6_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/6zj6 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/6zj6 | HTTPS FTP |
-Related structure data
Related structure data | 6zdcC 6zdfC 6zdkC 6zdlC 6zfaC 6zfnC 6zfqC 6zj1C 6zj5C 6hmgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4288341 / Data set type: diffraction image data |
-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 / Sugars , 2 types, 2 molecules AAA
#1: Protein | Mass: 43933.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides xylanisolvens XB1A (bacteria) Gene: BXY_34140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6D1V7 |
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#6: Sugar | ChemComp-GLC / |
-Non-polymers , 5 types, 470 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-QTE / | #5: Chemical | ChemComp-IFM / | #7: 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: 2.23 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 3 M sodium acetate pH 6.6 - 7,4 / PH range: 6.6-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→76.35 Å / Num. obs: 153951 / % possible obs: 95.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 11.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.027 / Rrim(I) all: 0.065 / Χ2: 0.78 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.09→1.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5269 / CC1/2: 0.358 / Rpim(I) all: 0.715 / Rrim(I) all: 1.342 / Χ2: 0.43 / % possible all: 66.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HMG Resolution: 1.09→76.35 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.839 / SU ML: 0.017 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.024 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.312 Å2
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Refinement step | Cycle: LAST / Resolution: 1.09→76.35 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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