+Open data
-Basic information
Entry | Database: PDB / ID: 4zeb | ||||||||||||
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Title | PBP AccA from A. tumefaciens C58 in complex with agrocinopine A | ||||||||||||
Components | ABC transporter, substrate binding protein (Agrocinopines A and B) | ||||||||||||
Keywords | TRANSPORT PROTEIN / PBP / CLASS C | ||||||||||||
Function / homology | Function and homology information dipeptide transport / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 | 4zeb.cif.gz | 413.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zeb.ent.gz | 336.3 KB | Display | PDB format |
PDBx/mmJSON format | 4zeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zeb_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4zeb_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4zeb_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 4zeb_validation.cif.gz | 59.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4zeb ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zeb | HTTPS FTP |
-Related structure data
Related structure data | 4ra1C 4ze8C 4ze9C 4zecC 4zedC 4zeiC 4zekC 4oup C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: 57178.102 Da / Num. of mol.: 2 / Fragment: UNP residues 30-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: accA, Atu6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7D2F4, UniProt: Q52012*PLUS |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Type: oligosaccharide / Mass: 422.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Sugar | |
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-Non-polymers , 3 types, 530 molecules
#4: Chemical | ChemComp-EDO / |
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#5: Chemical | ChemComp-PEG / |
#6: 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: 2.17 Å3/Da / Density % sol: 43.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 20K, 0.1M MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K PH range: 6.5 |
-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: Dec 13, 2012 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 78059 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 33.48 Å2 / Rsym value: 0.111 / Net I/σ(I): 7.87 |
Reflection shell | Resolution: 1.89→2.01 Å / Rsym value: 0.926 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OUP 4oup Resolution: 1.89→37.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 36.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.246 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→37.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.94 Å / 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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