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Yorodumi- PDB-6ght: HtxB D206A protein variant from Pseudomonas stutzeri in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ght | ||||||
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Title | HtxB D206A protein variant from Pseudomonas stutzeri in complex with hypophosphite to 1.12 A resolution | ||||||
Components | Probable phosphite transport system-binding protein HtxB | ||||||
Keywords | TRANSPORT PROTEIN / Periplasmic binding protein / phosphite / hypophosphite / ABC-transporter | ||||||
Function / homology | Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ACETIC ACID / FORMIC ACID / phosphinate / Probable phosphite transport system-binding protein HtxB Function and homology information | ||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Bisson, C. / Robertson, A.J. / Hitchcock, A. / Adams, N.B. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Phosphite binding by the HtxB periplasmic binding protein depends on the protonation state of the ligand. Authors: Adams, N.B.P. / Robertson, A.J. / Hunter, C.N. / Hitchcock, A. / Bisson, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ght.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ght.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ght.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ght_validation.pdf.gz | 464.7 KB | Display | wwPDB validaton report |
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Full document | 6ght_full_validation.pdf.gz | 466 KB | Display | |
Data in XML | 6ght_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 6ght_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/6ght ftp://data.pdbj.org/pub/pdb/validation_reports/gh/6ght | HTTPS FTP |
-Related structure data
Related structure data | 6emnC 6ghqC 5me4S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30290.525 Da / Num. of mol.: 1 / Mutation: D206A Source method: isolated from a genetically manipulated source Details: C-terminal 6xHis tag D206A mutation / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: htxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69061 |
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-Non-polymers , 5 types, 247 molecules
#2: Chemical | ChemComp-FMT / |
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#3: Chemical | ChemComp-ACY / |
#4: Chemical | ChemComp-HP4 / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.54 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 and 25 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→50.64 Å / Num. obs: 108281 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.12→1.139 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5252 / CC1/2: 0.322 / Rpim(I) all: 1.59 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ME4 Resolution: 1.12→50.64 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.466 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.567 Å2
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Refinement step | Cycle: 1 / Resolution: 1.12→50.64 Å
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Refine LS restraints |
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