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- PDB-1pnz: Crystal structure of ferric citrate transporter FecA in the unlig... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pnz | ||||||
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Title | Crystal structure of ferric citrate transporter FecA in the unliganded form | ||||||
![]() | Iron(III) dicitrate transport protein fecA precursor | ||||||
![]() | MEMBRANE PROTEIN / outer membrane protein / beta barrel / TonB-dependent transport | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yue, W.W. / Grizot, S. / Buchanan, S.K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145 KB | Display | ![]() |
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PDB format | ![]() | 110.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.3 KB | Display | ![]() |
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Full document | ![]() | 439.2 KB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 37.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1po0C ![]() 1po3C ![]() 1kmoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 83169.328 Da / Num. of mol.: 1 / Fragment: FecA residues 81-741 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.51 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG1000, LDAO, sodium acetate, sodium chloride, pH 5.2, 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: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 17, 2002 |
Radiation | Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.87 Å / Num. all: 34927 / Num. obs: 34890 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.03 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.3 / Num. unique all: 3411 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 34966 / Num. measured all: 242541 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 3411 / Num. measured obs: 23997 / Rmerge(I) obs: 0.424 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB accession code 1KMO Resolution: 2.5→19.82 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Side chains were not built for residues ARG93, ASN531, GLN695 and MET696
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.7077 Å2 / ksol: 0.364499 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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