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Yorodumi- PDB-4ra1: PBP AccA from A. tumefaciens C58 in complex with D-Glucose-2-phosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ra1 | ||||||
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Title | PBP AccA from A. tumefaciens C58 in complex with D-Glucose-2-phosphate | ||||||
Components | ABC transporter, substrate binding protein (Agrocinopines A and B)ATP-binding cassette transporter | ||||||
Keywords | TRANSPORT PROTEIN / Periplasmic binding protein C cluster | ||||||
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: 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 | 4ra1.cif.gz | 219.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ra1.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ra1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/4ra1 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4ra1 | HTTPS FTP |
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-Related structure data
Related structure data | 4ze8C 4ze9C 4zebC 4zecC 4zedC 4zeiC 4zekC 4oux 4oup 4out 4ouv 4ouw 4ouy 4ouz 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57178.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (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, 2 molecules
#2: Sugar | ChemComp-ALX / |
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#3: Sugar | ChemComp-BNX / |
-Non-polymers , 3 types, 386 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | ALX AND BNX ARE IN ALTERNATE CONFORMATI |
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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: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4K, 0.2M NH4 Acetate, 0.1M NaCitrate, pH 5.6 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014 |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 51001 / Num. obs: 50794 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.73 Å2 |
Reflection shell | Resolution: 1.75→1.85 Å / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OUX 4oux Resolution: 1.75→42.45 Å / Cor.coef. Fo:Fc: 0.9422 / Cor.coef. Fo:Fc free: 0.9314 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→42.45 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: -16.5991 Å / Origin y: -26.3669 Å / Origin z: 14.5518 Å
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Refinement TLS group | Selection details: { A|32 - A|521 } |