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Yorodumi- PDB-5ovz: High resolution structure of the PBP NocT in complex with nopaline -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ovz | |||||||||
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Title | High resolution structure of the PBP NocT in complex with nopaline | |||||||||
Components | Nopaline-binding periplasmic protein | |||||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding protein | |||||||||
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 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å | |||||||||
Authors | Vigouroux, A. / Morera, S. | |||||||||
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 | 5ovz.cif.gz | 222.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ovz.ent.gz | 176.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ovz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/5ovz ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovz | HTTPS FTP |
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-Related structure data
Related structure data | 4p0iC 4powC 4pp0C 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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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 Source: (gene. exp.) Agrobacterium (bacteria) / Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: P35120 |
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-Non-polymers , 5 types, 305 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / #6: 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: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% P4000/ 0.1 M Tris pH 8/ 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: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 55776 / Num. obs: 224742 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 33.71 Å2 / CC1/2: 0.999 / Rsym value: 0.05 / Net I/σ(I): 14.18 |
Reflection shell | Resolution: 1.75→1.86 Å / Mean I/σ(I) obs: 1.41 / Num. measured obs: 35655 / Num. unique all: 8999 / CC1/2: 0.57 / Rsym value: 0.837 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4POX 4pox Resolution: 1.75→37.4 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.092
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Displacement parameters | Biso mean: 42.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→37.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 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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