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Yorodumi- PDB-2x26: Crystal structure of the periplasmic aliphatic sulphonate binding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x26 | ||||||
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Title | Crystal structure of the periplasmic aliphatic sulphonate binding protein SsuA from Escherichia coli | ||||||
Components | PERIPLASMIC ALIPHATIC SULPHONATES-BINDING PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information ABC-type alkanesulfonate transporter transporter activity / alkanesulfonate transmembrane transport / sulfur compound metabolic process / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / periplasmic space / membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Beale, J. / Lee, S. / Iwata, S. / Beis, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structure of the Aliphatic Sulfonate-Binding Protein Ssua from Escherichia Coli Authors: Beale, J. / Lee, S.Y. / Iwata, S. / Beis, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x26.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x26.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 2x26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x26_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 2x26_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 2x26_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 2x26_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/2x26 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x26 | HTTPS FTP |
-Related structure data
Related structure data | 3e4rS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33730.414 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-319 Source method: isolated from a genetically manipulated source Details: C-TERMINAL EXTENSION AFTER THE MATURE PROTEIN / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: GFPD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P75853 #2: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.72 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 22% PEG3350, 0.2M SODIUM FORMATE AT 293K IN 2 DAYS, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 16, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→71.2 Å / Num. obs: 57014 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3E4R Resolution: 1.75→79.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.671 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. RESIDUES 320 TO 332 BELONG TO THE C-TERMINAL EXTENSION FROM THE CLONING VECTOR. THERE IS STILL SOME POSITIVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. RESIDUES 320 TO 332 BELONG TO THE C-TERMINAL EXTENSION FROM THE CLONING VECTOR. THERE IS STILL SOME POSITIVE DENSITY OBSERVED AROUND RESIDUES B328-332. THIS IS BECAUSE WE HAVE MODELLED AND REFINED WITH 0.5 OCCUPANCY DUE TO CONFORMATION CHANGES.
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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: 13.746 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→79.62 Å
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Refine LS restraints |
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