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Yorodumi- PDB-5otc: Structure of the periplasmic binding protein (PBP) NocT from Agro... -
+Open data
-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. | ||||||
Components | Nopaline-binding periplasmic protein | ||||||
Keywords | PROTEIN BINDING / Agrobacterium tumefaciens / Arginine / Bacterial Proteins / DNA / Bacterial / Gene Expression Regulation / Genes / Ligands / Plant Tumors / Plasmids | ||||||
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: 2.2 Å | ||||||
Authors | Vigouroux, A. / Morera, S. | ||||||
Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5otc.cif.gz | 213.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5otc.ent.gz | 171.2 KB | Display | PDB format |
PDBx/mmJSON format | 5otc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/5otc ftp://data.pdbj.org/pub/pdb/validation_reports/ot/5otc | HTTPS FTP |
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-Related structure data
Related structure data | 5oreC 5orgC 5ot8C 5ot9C 5otaC 5itpS 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 Details: HHHHHH : Tag Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli (E. coli) / References: UniProt: P35120 |
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-Non-polymers , 6 types, 110 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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