+Open data
-Basic information
Entry | Database: PDB / ID: 6org | ||||||
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Title | Crystal structure of SpGH29 | ||||||
Components | Glycoside hydrolase | ||||||
Keywords | HYDROLASE / glycoside hydrolase | ||||||
Function / homology | Function and homology information alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae serotype 4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å | ||||||
Authors | Pluvinage, B. / Boraston, A.B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Two complementary alpha-fucosidases fromStreptococcus pneumoniaepromote complete degradation of host-derived carbohydrate antigens. Authors: Hobbs, J.K. / Pluvinage, B. / Robb, M. / Smith, S.P. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6org.cif.gz | 214 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6org.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 6org.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/6org ftp://data.pdbj.org/pub/pdb/validation_reports/or/6org | HTTPS FTP |
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-Related structure data
Related structure data | 6or4C 6orfC 6orhC 3eypS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51020.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria) Strain: ATCC BAA-334 / TIGR4 / Gene: SP_2146 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2US78 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | The sequence corresponds to a C-terminally truncated sample during crystallization. | |
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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: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 16 % PEG 3350, 0.15 M KCl, 1 mM DTT and 0.1 M Bis-Tris. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→41.54 Å / Num. obs: 93880 / % possible obs: 98 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.031 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.72→1.82 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 13538 / CC1/2: 0.94 / Rpim(I) all: 0.162 / % possible all: 96.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EYP Resolution: 1.72→41.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.493 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 61.64 Å2 / Biso mean: 20.93 Å2 / Biso min: 8.84 Å2
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Refinement step | Cycle: final / Resolution: 1.72→41.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.722→1.767 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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