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- PDB-5org: Structure of the periplasmic binding protein (PBP) OccJ from A. t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5org | ||||||
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Title | Structure of the periplasmic binding protein (PBP) OccJ from A. tumefaciens B6 in complex with octopine. | ||||||
![]() | Octopine-binding periplasmic protein | ||||||
![]() | Octopine-binding protein / 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 | ![]() | 215 KB | Display | ![]() |
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PDB format | ![]() | 170.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5oreC ![]() 5ot8C ![]() 5ot9C ![]() 5otaC ![]() 5otcC ![]() 4powS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27992.861 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: occT, occJ / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 283 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/6DB.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/6DB.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ACT / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.69 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 4000, 0.1M Tris pH8.5, 0.1M acetate NH4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→30 Å / Num. obs: 54705 / % possible obs: 99.6 % / Redundancy: 9.5 % / Biso Wilson estimate: 39.06 Å2 / Rsym value: 0.088 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.99→2.4 Å / Mean I/σ(I) obs: 1.7 / Num. unique all: 8556 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4POW Resolution: 1.99→29.14 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.121
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Displacement parameters | Biso mean: 46.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.99→29.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.04 Å / Rfactor Rfree error: 0 / 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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