+Open data
-Basic information
Entry | Database: PDB / ID: 4z3p | ||||||
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Title | MATE transporter ClbM in complex with Rb+ | ||||||
Components | Putative drug/sodium antiporter | ||||||
Keywords | TRANSPORT PROTEIN / transporter | ||||||
Function / homology | Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / membrane / CACODYLATE ION / RUBIDIUM ION / Drug/sodium antiporter Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Mousa, J.J. / Bruner, S.D. | ||||||
Citation | Journal: Nat Microbiol / Year: 2016 Title: MATE transport of the E. coli-derived genotoxin colibactin. Authors: Mousa, J.J. / Yang, Y. / Tomkovich, S. / Shima, A. / Newsome, R.C. / Tripathi, P. / Oswald, E. / Bruner, S.D. / Jobin, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z3p.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z3p.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z3p_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 4z3p_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 4z3p_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 4z3p_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/4z3p ftp://data.pdbj.org/pub/pdb/validation_reports/z3/4z3p | HTTPS FTP |
-Related structure data
Related structure data | 4z3nC 3vvnS C: citing same article (ref.) S: Starting model for refinement |
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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: 55264.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clbM / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q0P7K3 |
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#2: Chemical | ChemComp-RB / |
#3: Chemical | ChemComp-CAC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.24 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.8 Details: 30% PEG 500 DME, 100 mM lithium sulfate, 400 mM rubidium chloride, 100 mM sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→43.81 Å / Num. obs: 10052 / % possible obs: 97.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.3→3.56 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.3 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VVN Resolution: 3.3→39.099 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→39.099 Å
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Refine LS restraints |
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LS refinement shell |
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