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Yorodumi- PDB-4mlb: Reverse polarity of binding pocket suggests different function of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mlb | ||||||
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Title | Reverse polarity of binding pocket suggests different function of a MOP superfamily transporter from Pyrococcus furiosus Vc1 (DSM3638) | ||||||
Components | PF0708 | ||||||
Keywords | TRANSPORT PROTEIN / lipid translocase / flippase / membrane protein | ||||||
Function / homology | : / : / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / plasma membrane / PENTAETHYLENE GLYCOL MONODECYL ETHER / MATE family efflux transporter Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 Å | ||||||
Authors | Malviya, V.N. / Nonaka, T. / Muenke, C. / Koepke, J. / Michel, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Inward-facing conformation of a multidrug resistance MATE family transporter. Authors: Zakrzewska, S. / Mehdipour, A.R. / Malviya, V.N. / Nonaka, T. / Koepke, J. / Muenke, C. / Hausner, W. / Hummer, G. / Safarian, S. / Michel, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mlb.cif.gz | 372.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mlb.ent.gz | 305.5 KB | Display | PDB format |
PDBx/mmJSON format | 4mlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mlb_validation.pdf.gz | 7.7 MB | Display | wwPDB validaton report |
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Full document | 4mlb_full_validation.pdf.gz | 7.8 MB | Display | |
Data in XML | 4mlb_validation.xml.gz | 70.3 KB | Display | |
Data in CIF | 4mlb_validation.cif.gz | 93.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/4mlb ftp://data.pdbj.org/pub/pdb/validation_reports/ml/4mlb | HTTPS FTP |
-Related structure data
Related structure data | 6fhzC 6gwhC 6hfbC 3mktS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 52928.137 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U2X0 #2: Chemical | ChemComp-CXE / #3: Chemical | #4: 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: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10 mg/ml protein, 0.1 M ADA/NaOH, pH 6.5, 10 mM ytterbium chloride, 0.15% w/v OG-Se, 24% w/v PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.17 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2008 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.17 Å / Relative weight: 1 |
Reflection | Resolution: 2.349→47.27 Å / Num. all: 95646 / Num. obs: 95103 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.349→2.48 Å / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MKT Resolution: 2.349→45.24 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 23.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.304 Å2 / ksol: 0.319 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.349→45.24 Å
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Refine LS restraints |
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LS refinement shell |
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