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Yorodumi- PDB-7sf6: Crystal Structure of Siderophore Binding Protein FatB from Desulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sf6 | ||||||
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Title | Crystal Structure of Siderophore Binding Protein FatB from Desulfitobacterium hafniense | ||||||
Components | Ferric-anguibactin-binding protein FatB | ||||||
Keywords | METAL TRANSPORT / siderophore / siderophore binding protein / periplasmic binding protein / Midwest Center for Structural Genomics / PSI-Biology / MCSG | ||||||
Function / homology | FatB domain / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / iron ion transport / Chem-DBS / : / Periplasmic binding protein Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Kim, Y. / Patel, H.P. / Nordquist, K.A. / Schaab, K.M. / Sha, J. / Babnigg, G. / Bond, A.H. / Joachimiak, A. / Midwest Center for Structural Genomics / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Siderophore Binding Protein FatB from Desulfitobacterium hafniense Authors: Kim, Y. / Patel, H.P. / Nordquist, K.A. / Schaab, K.M. / Sha, J. / Babnigg, G. / Bond, A.H. / Joachimiak, A. / Midwest Center for Structural Genomics | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sf6.cif.gz | 175.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sf6.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 7sf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/7sf6 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/7sf6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 33648.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense (bacteria) Gene: Dhaf_2916 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: B8FYL6 |
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-Non-polymers , 6 types, 410 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Chemical | ChemComp-FE / | #6: Chemical | #7: 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: 3.27 Å3/Da / Density % sol: 62.35 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.1M Bis-Tris propane pH 7.8, 2.5M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97891 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. obs: 76947 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 1.46→1.49 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 3778 / CC1/2: 0.759 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: swissmodel Resolution: 1.46→29.83 Å / SU ML: 0.1526 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.348 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: 21.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→29.83 Å
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Refine LS restraints |
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LS refinement shell |
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