+Open data
-Basic information
Entry | Database: PDB / ID: 6phu | ||||||
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Title | SpAga wild type apo structure | ||||||
Components | Alpha-galactosidase | ||||||
Keywords | HYDROLASE / (alpha/beta)8 barrel / glycoside hydrolase | ||||||
Function / homology | Function and homology information alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae serotype 4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Pluvinage, B. / Boraston, A.B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Molecular analysis of an enigmaticStreptococcus pneumoniaevirulence factor: The raffinose-family oligosaccharide utilization system. Authors: Hobbs, J.K. / Meier, E.P.W. / Pluvinage, B. / Mey, M.A. / 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 | 6phu.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6phu.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 6phu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6phu_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 6phu_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 6phu_validation.xml.gz | 30 KB | Display | |
Data in CIF | 6phu_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/6phu ftp://data.pdbj.org/pub/pdb/validation_reports/ph/6phu | HTTPS FTP |
-Related structure data
Related structure data | 6phvC 6phwC 6phxC 6phyC 6pi0C 6pqlC 6preC 6prgC 4fnuS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 83968.172 Da / Num. of mol.: 1 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: aga, SP_1898 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2URQ6, alpha-galactosidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TLA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate:acetic acid, 1.1 M ammonium tartrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5419 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 44566 / % possible obs: 99.2 % / Redundancy: 4.7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.077 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3731 / CC1/2: 0.805 / Rpim(I) all: 0.244 / % possible all: 98.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FNU Resolution: 2.2→29.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.265 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.203 / 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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93 Å2 / Biso mean: 34.826 Å2 / Biso min: 20.84 Å2
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Refinement step | Cycle: final / Resolution: 2.2→29.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.255 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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