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Yorodumi- PDB-7ofx: Crystal structure of a GH31 family sulfoquinovosidase mutant D455... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ofx | ||||||
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Title | Crystal structure of a GH31 family sulfoquinovosidase mutant D455N from Agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (SQGro) | ||||||
Components | Alpha-glucosidase yihQ | ||||||
Keywords | HYDROLASE / sulfoquinovose / SQGro / sulfoquinovosyl glycerol / SQDG / sulfoglycolysis / sulfo-EMP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhizobium radiobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Sharma, M. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / ...Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / Ascher, D.B. / McConville, M.J. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ofx.cif.gz | 509.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ofx.ent.gz | 416.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ofx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ofx_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7ofx_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7ofx_validation.xml.gz | 86.2 KB | Display | |
Data in CIF | 7ofx_validation.cif.gz | 123.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/7ofx ftp://data.pdbj.org/pub/pdb/validation_reports/of/7ofx | HTTPS FTP |
-Related structure data
Related structure data | 7bbyC 7bbzC 7bc0C 7bc1C 7nbzC 7ofyC 7oh2C 7olfC 5ohtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 75231.438 Da / Num. of mol.: 4 / Mutation: D455N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: SY94_3281 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A083ZKV2, alpha-glucosidase #2: Chemical | ChemComp-VCW / [( #3: Water | ChemComp-HOH / | 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: 2.49 Å3/Da / Density % sol: 50.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 24% PEG 3350 w/v, 0.2 M KSCN, 0.1 M Bis-Tris propane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 28, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.15→61.51 Å / Num. obs: 153301 / % possible obs: 97.4 % / Redundancy: 2.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.061 / Rrim(I) all: 0.109 / Net I/σ(I): 8.1 / Num. measured all: 442708 / Scaling rejects: 162 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.9 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OHT Resolution: 2.15→61.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.942 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.187 / 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 max: 111.95 Å2 / Biso mean: 28.618 Å2 / Biso min: 2.84 Å2
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Refinement step | Cycle: final / Resolution: 2.15→61.01 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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