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Yorodumi- PDB-6hs3: Crystal structure of an ABC transporter related protein from Burk... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hs3 | |||||||||
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Title | Crystal structure of an ABC transporter related protein from Burkholderia pseudomallei | |||||||||
Components | ABC transporter family protein | |||||||||
Keywords | CYTOSOLIC PROTEIN / ABC transporter / Burkholderia pseudomallei / transport protein / ATP-binding protein | |||||||||
Function / homology | Function and homology information ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / hydrolase activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Burkholderia pseudomallei (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Pankov, G. / Hunter, W.N. / Dawson, A. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: The structure of lipopolysaccharide transport protein B (LptB) from Burkholderia pseudomallei. Authors: Pankov, G. / Dawson, A. / Hunter, W.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hs3.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hs3.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hs3_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 6hs3_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 6hs3_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 6hs3_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/6hs3 ftp://data.pdbj.org/pub/pdb/validation_reports/hs/6hs3 | HTTPS FTP |
-Related structure data
Related structure data | 4wbsS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 13 - 255 / Label seq-ID: 15 - 257
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-Components
#1: Protein | Mass: 28352.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GH in the beginning of the sequence is left from cleaving N-terminal His-tag Source: (gene. exp.) Burkholderia pseudomallei (bacteria) Gene: lptB_3, lptB, BOC42_17415, CXQ84_18695, DP46_1122, DP49_575, ERS012350_00705 Plasmid: pET15b-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069AY91, UniProt: Q63XK6*PLUS #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: 2.15 Å3/Da / Density % sol: 42.75 % Description: Crystals appear within 24h and look like needles growing in multiple directions from a single nucleation point |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein buffer: 50 mM HEPES pH 7.0, 150 mM NaCl, 5 mM MgCl2, 500 uM ATP Crystallisation condition: 0.2 M MgCl2, 0.1 M Tris-HCL pH 8.5, 30 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96858 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.49 Å / Num. obs: 19107 / % possible obs: 97 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.103 / Rrim(I) all: 0.159 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1977 / CC1/2: 0.487 / Rpim(I) all: 0.496 / Rrim(I) all: 0.941 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WBS Resolution: 2.4→29.51 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.865 / SU B: 10.078 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.636 / ESU R Free: 0.31 / 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: 28.814 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→29.51 Å
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