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- PDB-5otc: Structure of the periplasmic binding protein (PBP) NocT from Agro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5otc | ||||||
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Title | Structure of the periplasmic binding protein (PBP) NocT from Agrobacterium tumefaciens C58 in complex with noroctopinic acid. | ||||||
![]() | Nopaline-binding periplasmic protein | ||||||
![]() | PROTEIN BINDING / Agrobacterium tumefaciens / Arginine / Bacterial Proteins / DNA / Bacterial / Gene Expression Regulation / Genes / Ligands / Plant Tumors / Plasmids | ||||||
Function / homology | ![]() nitrogen compound transport / ligand-gated monoatomic ion channel activity / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vigouroux, A. / Morera, S. | ||||||
![]() | ![]() Title: Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens. Authors: Vigouroux, A. / El Sahili, A. / Lang, J. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / Morera, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.9 KB | Display | ![]() |
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PDB format | ![]() | 171.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.9 KB | Display | ![]() |
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Full document | ![]() | 480.9 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oreC ![]() 5orgC ![]() 5ot8C ![]() 5ot9C ![]() 5otaC ![]() 5itpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 29259.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HHHHHH : Tag Source: (gene. exp.) ![]() Strain: C58 / ATCC 33970 / Gene: nocT, Atu6027, AGR_pTi_67 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 110 molecules ![](data/chem/img/AQK.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4K, 100 mM Tris pH 8.5 and 0.1 mM LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 27945 / % possible obs: 99.5 % / Redundancy: 8.5 % / Biso Wilson estimate: 53.88 Å2 / Rsym value: 0.075 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.2→2.33 Å / Mean I/σ(I) obs: 1.3 / Rsym value: 1.196 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ITP Resolution: 2.2→37.31 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.233 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.175
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Displacement parameters | Biso mean: 60.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→37.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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