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Yorodumi- PDB-4zed: PBP AccA from A. tumefaciens C58 in complex with agrocinopine-3'-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zed | ||||||
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Title | PBP AccA from A. tumefaciens C58 in complex with agrocinopine-3'-O-benzoate | ||||||
Components | ABC transporter, substrate binding protein (Agrocinopines A and B)ATP-binding cassette transporter | ||||||
Keywords | TRANSPORT PROTEIN / PBP / CLASS C | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | El Sahili, A. / Morera, S. | ||||||
Citation | Journal: Plos Pathog. / Year: 2015 Title: A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. Authors: El Sahili, A. / Li, S.Z. / Lang, J. / Virus, C. / Planamente, S. / Ahmar, M. / Guimaraes, B.G. / Aumont-Nicaise, M. / Vigouroux, A. / Soulere, L. / Reader, J. / Queneau, 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 | 4zed.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zed.ent.gz | 185.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4zed ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zed | HTTPS FTP |
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-Related structure data
Related structure data | 4ra1C 4ze8C 4ze9C 4zebC 4zecC 4zeiC 4zekC 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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Unit cell |
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-Components
#1: Protein | Mass: 57178.102 Da / Num. of mol.: 1 / Fragment: UNP residues 30-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (strain C58 / ATCC 33970) (bacteria) Gene: accA, Atu6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7D2F4, UniProt: Q52012*PLUS |
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#2: Chemical | ChemComp-AGW / [( |
#3: Chemical | ChemComp-EDO / |
#4: 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: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% P4K, 0.2M ACETATE NH4, 0.1M CITRATE NA PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å | |||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2013 | |||||||||
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→50 Å / Num. obs: 51499 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 11.5 % / Biso Wilson estimate: 28.67 Å2 / Rsym value: 0.092 / Net I/σ(I): 12.25 | |||||||||
Reflection shell | Resolution: 1.75→1.85 Å / Rsym value: 0.844 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Resolution: 1.75→42.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.097
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Displacement parameters | Biso mean: 29.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.225 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→42.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -16.5043 Å / Origin y: -26.7053 Å / Origin z: 14.5401 Å
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Refinement TLS group | Selection details: A 32 A 521 |