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Yorodumi- PDB-5ito: Structure of the periplasmic binding protein M117N-NocT from A. t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ito | ||||||
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Title | Structure of the periplasmic binding protein M117N-NocT from A. tumefaciens in complex with octopine | ||||||
Components | Nopaline-binding periplasmic protein | ||||||
Keywords | MEMBRANE PROTEIN / Periplasmic binding protein / opine / octopine | ||||||
Function / homology | Function and homology information nitrogen compound transport / ligand-gated monoatomic ion channel activity / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | Agrobacterium fabrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Vigouroux, A. / Morera, S. | ||||||
Funding support | France, 1items
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Citation | Journal: ISME J / Year: 2017 Title: Fitness costs restrict niche expansion by generalist niche-constructing pathogens. Authors: Lang, J. / Vigouroux, A. / El Sahili, A. / Kwasiborski, A. / Aumont-Nicaise, M. / Dessaux, Y. / Shykoff, J.A. / 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 | 5ito.cif.gz | 213 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ito.ent.gz | 168.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ito.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/5ito ftp://data.pdbj.org/pub/pdb/validation_reports/it/5ito | HTTPS FTP |
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-Related structure data
Related structure data | 5itpC 4pox 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29242.533 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli (E. coli) / References: UniProt: P35120 |
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-Non-polymers , 6 types, 104 molecules
#2: Chemical | ChemComp-PEG / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-1PE / | #5: Chemical | #6: Chemical | #7: 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: 2.53 Å3/Da / Density % sol: 51.36 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4K, 0.1 M Tris pH8, 0.1 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→49 Å / Num. obs: 22829 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 56.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.35→2.49 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.97 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4POX 4pox Resolution: 2.35→25.98 Å / Cor.coef. Fo:Fc: 0.9558 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.206
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Displacement parameters | Biso mean: 53.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.305 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→25.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.46 Å / Total num. of bins used: 11
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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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