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Yorodumi- PDB-6bl6: Crystallization of lipid A transporter MsbA from Salmonella typhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bl6 | |||||||||
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Title | Crystallization of lipid A transporter MsbA from Salmonella typhimurium | |||||||||
Components | Lipid A export ATP-binding/permease protein MsbA | |||||||||
Keywords | MEMBRANE PROTEIN / MsbA / Lipid A co-crystallization / ABC transporters / Staphylococcus typhimurium | |||||||||
Function / homology | Function and homology information ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Padayatti, P.S. / Stanfield, R.L. / Zhang, Q. / Wilson, I.A. / Lee, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2019 Title: Structural Insights into the Lipid A Transport Pathway in MsbA. Authors: Padayatti, P.S. / Lee, S.C. / Stanfield, R.L. / Wen, P.C. / Tajkhorshid, E. / Wilson, I.A. / Zhang, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bl6.cif.gz | 228.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bl6.ent.gz | 183.4 KB | Display | PDB format |
PDBx/mmJSON format | 6bl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/6bl6 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/6bl6 | HTTPS FTP |
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-Related structure data
Related structure data | 6o30C 3b5wS 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 7 - 581 / Label seq-ID: 1 - 575
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-Components
#1: Protein | Mass: 63607.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: msbA, STM0984 / Variant: SGSC1412 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P63359, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
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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: 5.71 Å3/Da / Density % sol: 78.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MsbA purified in detergent micelles (UDM/FA231) is mixed with lipid A prior to crystallization and mixed 1: 1 with well solution 20 mM Tris-Hcl (pH 7.5) and 15-20 5 PEG 300 . Crystals appeared in month (approx.) PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: 80 |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127085 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127085 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50.01 Å / Num. obs: 60504 / % possible obs: 84.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 68.3 Å2 / CC1/2: 0.893 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.057 / Rrim(I) all: 0.148 / Χ2: 1.288 / Net I/av σ(I): 10 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.057 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B5W Resolution: 2.8→50.01 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.925 / SU B: 23.048 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R: 0.519 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.187 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→50.01 Å
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Refine LS restraints |
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