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Yorodumi- PDB-7bcr: Crystal structure of the sugar acid binding protein DctPAm from A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bcr | ||||||
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Title | Crystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with galactonate | ||||||
Components | Putative TRAP transporter solute receptor DctP | ||||||
Keywords | SUGAR BINDING PROTEIN / sugar acid substrate binding protein TRAP transporter | ||||||
Function / homology | TRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / L-galactonic acid / Putative TRAP transporter solute receptor DctP Function and homology information | ||||||
Biological species | Advenella mimigardefordensis DPN7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Schaefer, L. / Meinert, C. / Kobus, S. / Hoeppner, A. / Smits, S.H. / Steinbuechel, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Febs J. / Year: 2021 Title: Crystal structure of the sugar acid-binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7 T . Authors: Schafer, L. / Meinert-Berning, C. / Kobus, S. / Hoppner, A. / Smits, S.H.J. / Steinbuchel, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bcr.cif.gz | 162 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bcr.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bcr_validation.pdf.gz | 322 KB | Display | wwPDB validaton report |
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Full document | 7bcr_full_validation.pdf.gz | 325.6 KB | Display | |
Data in XML | 7bcr_validation.xml.gz | 17 KB | Display | |
Data in CIF | 7bcr_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/7bcr ftp://data.pdbj.org/pub/pdb/validation_reports/bc/7bcr | HTTPS FTP |
-Related structure data
Related structure data | 7bbrSC 7bcnC 7bcoC 7bcpC 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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Unit cell |
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-Components
#1: Protein | Mass: 37017.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Advenella mimigardefordensis DPN7 (bacteria) Gene: MIM_c39430 / Production host: Escherichia coli (E. coli) / References: UniProt: R4JTF7 |
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#2: Chemical | ChemComp-2Q2 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG4000 / PH range: 7.0-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.967 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.92 Å / Num. obs: 156928 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 27.81 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.49 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.22 / Num. unique obs: 15796 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BBR Resolution: 2→50.92 Å / SU ML: 0.2992 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.4672 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50.92 Å
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Refine LS restraints |
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LS refinement shell |
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