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Yorodumi- PDB-1esz: STRUCTURE OF THE PERIPLASMIC FERRIC SIDEROPHORE BINDING PROTEIN F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1esz | ||||||
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Title | STRUCTURE OF THE PERIPLASMIC FERRIC SIDEROPHORE BINDING PROTEIN FHUD COMPLEXED WITH COPROGEN | ||||||
Components | FERRICHROME-BINDING PERIPLASMIC PROTEIN | ||||||
Keywords | METAL TRANSPORT / FhuD / iron transport / siderophore binding protein / periplasmic ligand binding protein / ABC transport protein | ||||||
Function / homology | Function and homology information iron ion import across plasma membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Clarke, T.E. / Braun, V. / Winkelmann, G. / Tari, L.W. / Vogel, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: X-ray crystallographic structures of the Escherichia coli periplasmic protein FhuD bound to hydroxamate-type siderophores and the antibiotic albomycin. Authors: Clarke, T.E. / Braun, V. / Winkelmann, G. / Tari, L.W. / Vogel, H.J. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: The Structure of the Ferric Siderophore Binding Protein Fhud Complexed with Gallichrome Authors: Clarke, T.E. / Ku, S.-Y. / Dougan, D. / Vogel, H.J. / Tari, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1esz.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1esz.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1esz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1esz_validation.pdf.gz | 479.9 KB | Display | wwPDB validaton report |
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Full document | 1esz_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 1esz_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1esz_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1esz ftp://data.pdbj.org/pub/pdb/validation_reports/es/1esz | HTTPS FTP |
-Related 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: 29694.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: P07822 |
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#2: Chemical | ChemComp-CPO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.84 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Na/K phosphate, HEPES, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9787 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Feb 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 26445 / Num. obs: 25292 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 90.1 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 2→30 Å / Redundancy: 90.1 % / Rmerge(I) obs: 0.102 / % possible all: 95.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 90.1 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 6.6 |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / σ(F): 1 / σ(I): 2 Details: Average B factors as reported by the author- Ligand: 31.90 Waters: 35.76
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Displacement parameters | Biso mean: 28.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection Rfree: 1165 / Rfactor obs: 0.219 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.219 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |