+Open data
-Basic information
Entry | Database: PDB / ID: 4pp0 | ||||||
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Title | Structure of the PBP NocT-M117N in complex with pyronopaline | ||||||
Components | Nopaline-binding periplasmic protein | ||||||
Keywords | TRANSPORT PROTEIN / PBP / class F | ||||||
Function / homology | Function and homology information ligand-gated monoatomic ion channel activity / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Morera, S. / Vigouroux, A. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 Title: Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host. Authors: Lang, J. / Vigouroux, A. / Planamente, S. / El Sahili, A. / Blin, P. / Aumont-Nicaise, M. / Dessaux, Y. / Morera, S. / Faure, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pp0.cif.gz | 220.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pp0.ent.gz | 174.6 KB | Display | PDB format |
PDBx/mmJSON format | 4pp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pp0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4pp0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4pp0_validation.xml.gz | 27 KB | Display | |
Data in CIF | 4pp0_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/4pp0 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/4pp0 | HTTPS FTP |
-Related structure data
Related structure data | 4p0iC 4powC 5ovzC 4poiS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29242.533 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-283 / Mutation: M117N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli (E. coli) / References: UniProt: P35120 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 2.46 Å3/Da / Density % sol: 49.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4K, 0.1 M Tris, 0.1 M LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2013 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→23 Å / Num. all: 77700 / Num. obs: 77698 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 24.79 Å2 |
Reflection shell | Resolution: 1.57→1.66 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4POI Resolution: 1.57→22.99 Å / Cor.coef. Fo:Fc: 0.9677 / Cor.coef. Fo:Fc free: 0.9646 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.191 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→22.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.61 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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