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Yorodumi- PDB-4zek: PBP AccA from A. tumefaciens C58 in complex with L-arabinose-2-is... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zek | |||||||||
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Title | PBP AccA from A. tumefaciens C58 in complex with L-arabinose-2-isopropylphosphate | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.09 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 | 4zek.cif.gz | 214.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zek.ent.gz | 168.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4zek ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zek | HTTPS FTP |
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-Related structure data
Related structure data | 4ra1C 4ze8C 4ze9C 4zebC 4zecC 4zedC 4zeiC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 57178.102 Da / Num. of mol.: 1 / Fragment: unp residues 29-527 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Gene: ACCA, ATU6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52012*PLUS |
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#2: Sugar | ChemComp-LAH / |
-Non-polymers , 4 types, 207 molecules
#3: Chemical | #4: Chemical | ChemComp-TOE / | #5: Chemical | ChemComp-PEG / | #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: 2.17 Å3/Da / Density % sol: 43.2 % |
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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 |
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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: Sep 29, 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: 2.1→42.23 Å / Num. obs: 29355 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 37.37 Å2 / Rsym value: 0.182 / Net I/σ(I): 7.88 |
Reflection shell | Resolution: 2.1→2.22 Å / Rsym value: 1.304 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OUP 4oup Resolution: 2.09→42.2 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 40.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.281 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→42.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.16 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: -16.8244 Å / Origin y: -26.2477 Å / Origin z: 14.3479 Å
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Refinement TLS group | Selection details: A 32 A 521 |