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Yorodumi- PDB-3sev: Zn-mediated Trimer of Maltose-binding Protein E310H/K314H by Synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sev | |||||||||
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Title | Zn-mediated Trimer of Maltose-binding Protein E310H/K314H by Synthetic Symmetrization | |||||||||
Components | Maltose-binding periplasmic protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / metal-mediated synthetic symmetrization / synthetic symmetrization | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å | |||||||||
Authors | Zhao, M. / Soriaga, A.B. / Laganowsky, A. / Sawaya, M.R. / Cascio, D. / Yeates, T.O. | |||||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Authors: Laganowsky, A. / Zhao, M. / Soriaga, A.B. / Sawaya, M.R. / Cascio, D. / Yeates, T.O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sev.cif.gz | 217.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sev.ent.gz | 174.4 KB | Display | PDB format |
PDBx/mmJSON format | 3sev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/3sev ftp://data.pdbj.org/pub/pdb/validation_reports/se/3sev | HTTPS FTP |
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-Related structure data
Related structure data | 3sb5C 3sb6C 3sb7C 3sb8C 3sb9C 3sbaC 3sbbC 3serC 3sesC 3setC 3seuC 3sewC 3sexC 3seyC 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
#1: Protein | Mass: 40639.980 Da / Num. of mol.: 3 / Mutation: E310H, K314H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4034, JW3994, malE / Plasmid: pMal-a1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AEX9 #2: Polysaccharide | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 3.22 Å3/Da / Density % sol: 61.86 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M HEPES, 2.4M AMMONIUM SULFATE, pH 8.0, vapor diffusion, hanging drop, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.05→39.06 Å / Num. obs: 30645 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.039 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.39 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→39.06 Å / Cor.coef. Fo:Fc: 0.8883 / Cor.coef. Fo:Fc free: 0.8474 / Occupancy max: 1 / Occupancy min: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 151.43 Å2 / Biso mean: 51.6023 Å2 / Biso min: 11.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.562 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→39.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.16 Å / Total num. of bins used: 15
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