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Yorodumi- PDB-6tfx: Structure in P21 form of the PBP/SBP MoaA in complex with mannopi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tfx | ||||||
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Title | Structure in P21 form of the PBP/SBP MoaA in complex with mannopinic acid from A.tumefacien R10 | ||||||
Components | ABC transporter substrate-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Solute binding protein / periplasmic binding protein | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Rhizobium radiobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Morera, S. / Vigouroux, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2020 Title: Import pathways of the mannityl-opines into the bacterial pathogen Agrobacterium tumefaciens: structural, affinity and in vivo approaches. Authors: Vigouroux, A. / Dore, J. / Marty, L. / Aumont-Nicaise, M. / Legrand, P. / Dessaux, Y. / Vial, L. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tfx.cif.gz | 406.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tfx.ent.gz | 328.4 KB | Display | PDB format |
PDBx/mmJSON format | 6tfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/6tfx ftp://data.pdbj.org/pub/pdb/validation_reports/tf/6tfx | HTTPS FTP |
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-Related structure data
Related structure data | 6tfqSC 6tfsC 6tg2C 6tg3C 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55446.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: moaA, ddpA, A6U90_18755, At1D1609_52430, AtA6_55190 / Production host: Escherichia coli (E. coli) / References: UniProt: O50271 |
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-Non-polymers , 5 types, 832 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-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: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4K, 100 mM MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→47.56 Å / Num. obs: 134434 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.04 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.56→1.66 Å / Rmerge(I) obs: 0.947 / Num. unique obs: 21895 / CC1/2: 0.646 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TFQ Resolution: 1.56→47.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.072
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Displacement parameters | Biso max: 110.6 Å2 / Biso mean: 24.56 Å2 / Biso min: 10.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.56→47.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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