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Yorodumi- PDB-5dgx: 1.73 Angstrom resolution crystal structure of the ABC-ATPase doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dgx | ||||||
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Title | 1.73 Angstrom resolution crystal structure of the ABC-ATPase domain (residues 357-609) of lipid A transport protein (msbA) from Francisella tularensis subsp. tularensis SCHU S4 in complex with ADP | ||||||
Components | Lipid A export ATP-binding/permease protein MsbA | ||||||
Keywords | TRANSPORT PROTEIN / Lipid A transport protein / ABC transporter / ATP-binding and membrane protein / Francisella tularensis subsp. tularensis SCHU S4 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.73 Angstrom resolution crystal structure of the ABC-ATPase domain (residues 357-609) of lipid A transport protein (msbA) from Francisella tularensis subsp. tularensis SCHU S4 in complex with ADP Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dgx.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dgx.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dgx_validation.pdf.gz | 746.9 KB | Display | wwPDB validaton report |
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Full document | 5dgx_full_validation.pdf.gz | 748.3 KB | Display | |
Data in XML | 5dgx_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5dgx_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/5dgx ftp://data.pdbj.org/pub/pdb/validation_reports/dg/5dgx | HTTPS FTP |
-Related structure data
Related structure data | 2fgkS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27843.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain FSC 198) (bacteria) Strain: FSC 198 / Gene: msbA, FTF0109 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-magic References: UniProt: Q14JW6, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: protein: 8.2 mg/ml in 10 mM Tris-HCl pH 8.3 0.5 mM TCEP 10 mM ADP 10 mM MgCl2 crystallization: The Classics II F11 (71): 0.2 M NaCl 0.1 M Bis-Tris pH 6.5 25% (w/v) PEG 3350 cryo: crystallization condition |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2015 |
Radiation | Monochromator: single diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. obs: 23573 / % possible obs: 90.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 97.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2fgk Resolution: 1.73→21.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.98 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.13 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.581 Å2
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Refinement step | Cycle: 1 / Resolution: 1.73→21.94 Å
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