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Yorodumi- PDB-1po3: Crystal structure of ferric citrate transporter FecA in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1po3 | ||||||
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Title | Crystal structure of ferric citrate transporter FecA in complex with ferric citrate | ||||||
Components | Iron(III) dicitrate transport protein fecA precursor | ||||||
Keywords | MEMBRANE PROTEIN / outer membrane protein / beta barrel / TonB-dependent transport / citrate / siderophore / iron | ||||||
Function / homology | Function and homology information response to iron ion starvation / siderophore-iron transmembrane transporter activity / siderophore-dependent iron import into cell / signal transduction involved in regulation of gene expression / transmembrane transporter complex / cell outer membrane / signaling receptor activity / iron ion transport / intracellular iron ion homeostasis / regulation of DNA-templated transcription / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Yue, W.W. / Grizot, S. / Buchanan, S.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural evidence for iron-free citrate and ferric citrate binding to the TonB-dependent outer membrane transporter FecA Authors: Yue, W.W. / Grizot, S. / Buchanan, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1po3.cif.gz | 243.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1po3.ent.gz | 194.8 KB | Display | PDB format |
PDBx/mmJSON format | 1po3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1po3_validation.pdf.gz | 479.5 KB | Display | wwPDB validaton report |
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Full document | 1po3_full_validation.pdf.gz | 560.7 KB | Display | |
Data in XML | 1po3_validation.xml.gz | 57.2 KB | Display | |
Data in CIF | 1po3_validation.cif.gz | 76.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/1po3 ftp://data.pdbj.org/pub/pdb/validation_reports/po/1po3 | HTTPS FTP |
-Related structure data
Related structure data | 1pnzC 1po0C 1kmpS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The biological assembly is a monomer although asymmetric unit is an NCS-related dimer |
-Components
#1: Protein | Mass: 83169.328 Da / Num. of mol.: 2 / Fragment: FecA residues 95-741 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FECA OR B4291 / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P13036 #2: Chemical | ChemComp-FLC / #3: Chemical | ChemComp-FE / |
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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: 3.4 Å3/Da / Density % sol: 63.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG1000, LDAO, calcium chloride, Bis-Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: X9B / Wavelength: 0.9795 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 17, 2002 |
Radiation | Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→19.77 Å / Num. all: 33661 / Num. obs: 30446 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 78.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3036 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 30794 / % possible obs: 100 % / Num. measured all: 135112 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 3036 / Num. measured obs: 13363 / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB accession code 1KMP Resolution: 3.4→15 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: In chain A side chains were not built for residues GLN221, MET249, ARG336, GLN351, ARG385, MET396, TYR499, ASP503, GLU533, ARG582, THR600, GLU616, ASP622, TYR624, LYS668, GLN695 and LYS740. ...Details: In chain A side chains were not built for residues GLN221, MET249, ARG336, GLN351, ARG385, MET396, TYR499, ASP503, GLU533, ARG582, THR600, GLU616, ASP622, TYR624, LYS668, GLN695 and LYS740. In chain B side chains were not built for residues ARG217, ASP222, MET249, HIS295, GLU307, PHE346, GLN351, ARG385, MET396, GLN428, TYR436, LYS454, MET466, GLU485, GLU533, ASP548, TYR592, LYS620 and MET696.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.268617 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.61 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.4 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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