+Open data
-Basic information
Entry | Database: PDB / ID: 1kmo | ||||||
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Title | Crystal structure of the Outer Membrane Transporter FecA | ||||||
Components | Iron(III) dicitrate transport protein fecA | ||||||
Keywords | MEMBRANE PROTEIN / Iron transporter / TonB-dependent receptor / Siderophore | ||||||
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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ferguson, A.D. / Chakraborty, R. / Smith, B.S. / Esser, L. / van der Helm, D. / Deisenhofer, J. | ||||||
Citation | Journal: Science / Year: 2002 Title: Structural basis of gating by the outer membrane transporter FecA. Authors: Ferguson, A.D. / Chakraborty, R. / Smith, B.S. / Esser, L. / van der Helm, D. / Deisenhofer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kmo.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kmo.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kmo_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 1kmo_full_validation.pdf.gz | 481 KB | Display | |
Data in XML | 1kmo_validation.xml.gz | 33.5 KB | Display | |
Data in CIF | 1kmo_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/1kmo ftp://data.pdbj.org/pub/pdb/validation_reports/km/1kmo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer which is contained within the asymmetric unit |
-Components
#1: Protein | Mass: 85406.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Ferric citrate uptake receptor / Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: k-12 / Gene: fecA / Plasmid: pSV66 / Production host: Escherichia coli (E. coli) / Strain (production host): UT5600 / References: UniProt: P13036 | ||||
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#2: Chemical | ChemComp-LDA / #3: Chemical | #4: 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: 2.85 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 1000, MOPS, LDAO, heptane-1,2,3-triol, sodium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 284K |
Crystal grow | *PLUS Details: Smith, B.S., (1998) Acta Cryst., D54, 697., Doublie, S., (1997) Methods Enzymol., 276, 532. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2000 |
Radiation | Monochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 56331 / Num. obs: 56331 / % possible obs: 92.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2→2.13 Å / % possible all: 0.71 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 62452 / Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 223348.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.2134 Å2 / ksol: 0.365878 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.4 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.327 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.28 |