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Yorodumi- PDB-1kmp: Crystal structure of the Outer Membrane Transporter FecA Complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kmp | ||||||
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Title | Crystal structure of the Outer Membrane Transporter FecA Complexed with Ferric Citrate | ||||||
Components | IRON(III) DICITRATE TRANSPORT PROTEIN FECA | ||||||
Keywords | MEMBRANE PROTEIN / Integral outer membrane protein / TonB-dependent receptor / 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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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 | 1kmp.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kmp.ent.gz | 120.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kmp_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 1kmp_full_validation.pdf.gz | 501.4 KB | Display | |
Data in XML | 1kmp_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 1kmp_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/1kmp ftp://data.pdbj.org/pub/pdb/validation_reports/km/1kmp | 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 of this protein is a monomer which is complete within the asymmetric unit |
-Components
#1: Protein | Mass: 86109.695 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 | #3: Chemical | #4: Chemical | ChemComp-LDA / #5: 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: 2.88 Å3/Da / Density % sol: 57.24 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 1000, MOPS, sodium chloride, LDAO, heptane-1,2,3-triol, glycerol, 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: APS / Beamline: 19-BM / Wavelength: 1.0003 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2001 / Details: Synchrotron |
Radiation | Monochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0003 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 57464 / Num. obs: 57464 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.5→2.66 Å / % possible all: 0.723 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 34980 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: Phase information was derived from an additional selenomethionyl derivative Resolution: 2.5→36.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 470835.04 / 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: 48.6268 Å2 / ksol: 0.375823 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→36.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / 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: 25 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.39 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.353 |