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Yorodumi- PDB-3seu: Zn-mediated Polymer of Maltose-binding Protein A216H/K220H by Syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3seu | |||||||||
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Title | Zn-mediated Polymer of Maltose-binding Protein A216H/K220H by Synthetic Symmetrization (Form III) | |||||||||
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 transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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: 1.85 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 | 3seu.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3seu.ent.gz | 130.8 KB | Display | PDB format |
PDBx/mmJSON format | 3seu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3seu_validation.pdf.gz | 848.2 KB | Display | wwPDB validaton report |
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Full document | 3seu_full_validation.pdf.gz | 849.9 KB | Display | |
Data in XML | 3seu_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 3seu_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/3seu ftp://data.pdbj.org/pub/pdb/validation_reports/se/3seu | HTTPS FTP |
-Related structure data
Related structure data | 3sb5C 3sb6C 3sb7C 3sb8C 3sb9C 3sbaC 3sbbC 3serC 3sesC 3setC 3sevC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 40698.020 Da / Num. of mol.: 1 / Mutation: A216H, K220H 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 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 4 types, 207 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / | #6: 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: 2.1 Å3/Da / Density % sol: 41.38 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M IMIDAZOLE, 0.2M ZINC ACETATE, 20% (W/V) PEG 3000, 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: 1.85→56.389 Å / Num. obs: 28565 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.643 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.85→56.389 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8809 / SU ML: 0.19 / σ(F): 1.99 / Phase error: 19.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.632 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.43 Å2 / Biso mean: 26.1604 Å2 / Biso min: 9.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→56.389 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 9.9571 Å / Origin y: -10.8889 Å / Origin z: 6.6907 Å
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Refinement TLS group | Selection details: ALL |