+Open data
-Basic information
Entry | Database: PDB / ID: 4zec | |||||||||
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Title | PBP AccA from A. tumefaciens C58 in complex with agrocin 84 | |||||||||
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 fabrum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 | 4zec.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zec.ent.gz | 170.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4zec ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zec | HTTPS FTP |
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-Related structure data
Related structure data | 4ra1C 4ze8C 4ze9C 4zebC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55960.781 Da / Num. of mol.: 1 / Fragment: UNP residues 30-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: accA, Atu6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52012 |
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-Non-polymers , 5 types, 231 molecules
#2: Chemical | ChemComp-C84 / [( | ||
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#3: Chemical | ChemComp-PEG / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4K, 0.2M ACNH4, 0.1M NA CITRATE PH 5.6 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: May 17, 2013 |
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: 2.147→45 Å / Num. obs: 26755 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 36.95 Å2 / Rsym value: 0.2 / Net I/σ(I): 8.24 |
Reflection shell | Resolution: 2.147→2.28 Å / Num. unique obs: 4191 / Rsym value: 1.04 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OUP 4oup Resolution: 2.15→42.06 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.205
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Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→42.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.17 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: -16.7464 Å / Origin y: -26.2935 Å / Origin z: 14.3506 Å
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Refinement TLS group | Selection details: { A|* } |