+Open data
-Basic information
Entry | Database: PDB / ID: 6pi6 | ||||||
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Title | The evolving story of AtzT, a periplasmic binding protein | ||||||
Components | Atrazine periplasmic binding protein | ||||||
Keywords | TRANSPORT PROTEIN / SAD phasing / periplasmic binding protein / evolution from purine binding to atrazine binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Peat, T.S. / Newman, J. / Scott, C. / Esquirol, L. / Dennis, M. / Nebl, T. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: The evolving story of AtzT, a periplasmic binding protein. Authors: Dennis, M.L. / Esquirol, L. / Nebl, T. / Newman, J. / Scott, C. / Peat, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pi6.cif.gz | 281.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pi6.ent.gz | 224.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pi6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6pi6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6pi6_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 6pi6_validation.cif.gz | 78.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/6pi6 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/6pi6 | HTTPS FTP |
-Related structure data
Related structure data | 6pi5C 6piiSC 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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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 38291.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (strain ADP) (bacteria) Strain: ADP / Gene: orf97, AOX63_31690 / Production host: Escherichia coli (E. coli) / References: UniProt: Q936X6 #2: Chemical | ChemComp-OKM / #3: Chemical | ChemComp-DMS / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein at 20 mg/mL in SD2 plates incubated at 20 C. Crystallisation conditions contained 6-8% Jeffamine M600 with 2-7% MPD and trisodium citrate at 1.1-1.2 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953716 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953716 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→49.1 Å / Num. obs: 176707 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 7 % / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8668 / CC1/2: 0.653 / Rpim(I) all: 0.515 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PII Resolution: 1.65→49.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.984 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.079 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 93.06 Å2 / Biso mean: 27.596 Å2 / Biso min: 14.75 Å2
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Refinement step | Cycle: final / Resolution: 1.65→49.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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