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Yorodumi- PDB-3qpf: Analysis of a New Family of Widely Distributed Metal-independent ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qpf | ||||||
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Title | Analysis of a New Family of Widely Distributed Metal-independent alpha-Mannosidases Provides Unique Insight into the Processing of N-linked Glycans, Streptococcus pneumoniae SP_2144 apo-structure | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | HYDROLASE / alpha-alpha six fold / Glycoside hydrolase / Mannosidase / Streptococcus pneumoniae | ||||||
Function / homology | Function and homology information carbohydrate catabolic process / catalytic activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Gregg, K.J. / Zandberg, W.F. / Hehemann, J.-H. / Whitworth, G.E. / Deng, L.E. / Vocadlo, D.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Analysis of a New Family of Widely Distributed Metal-independent {alpha}-Mannosidases Provides Unique Insight into the Processing of N-Linked Glycans. Authors: Gregg, K.J. / Zandberg, W.F. / Hehemann, J.H. / Whitworth, G.E. / Deng, L. / Vocadlo, D.J. / 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 | 3qpf.cif.gz | 201 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qpf.ent.gz | 160 KB | Display | PDB format |
PDBx/mmJSON format | 3qpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/3qpf ftp://data.pdbj.org/pub/pdb/validation_reports/qp/3qpf | HTTPS FTP |
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-Related 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: 49105.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_2144 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: Q97NA8, UniProt: A0A0H2URZ6*PLUS #2: Chemical | ChemComp-EDO / #3: 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: 2.47 Å3/Da / Density % sol: 50.15 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Hepes, 1.2 M LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 117 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2010 / Details: Rh coated flat mirror, toroidal focusing mirror |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→85.6 Å / Num. all: 50972 / Num. obs: 50972 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.15→2.27 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.371 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.724 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→48.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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