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Yorodumi- PDB-1qff: E. COLI FERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) IN COMPLEX WITH... -
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-Basic information
Entry | Database: PDB / ID: 1qff | |||||||||
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Title | E. COLI FERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) IN COMPLEX WITH BOUND FERRICHROME-IRON | |||||||||
Components | FERRIC HYDROXAMATE UPTAKE RECEPTOR | |||||||||
Keywords | METAL TRANSPORT / TONB-DEPENDENT RECEPTOR / INTEGRAL OUTER MEMBRANE PROTEIN / SIDEROPHORE-IRON RECEPTOR / ACTIVE TRANSPORT / LIPOPOLYSACCHARIDE / FERRICHROME RECEPTOR | |||||||||
Function / homology | Function and homology information siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virion binding / toxic substance binding / transmembrane transporter complex / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / iron ion binding / protein domain specific binding / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | |||||||||
Authors | Ferguson, A.D. / Hofmann, E. / Coulton, J.W. / Diederichs, K. / Welte, W. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins. Authors: Ferguson, A.D. / Welte, W. / Hofmann, E. / Lindner, B. / Holst, O. / Coulton, J.W. / Diederichs, K. #1: Journal: Science / Year: 1998 Title: Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide. Authors: Ferguson, A.D. / Hofmann, E. / Coulton, J.W. / Diederichs, K. / Welte, W. #2: Journal: Protein Sci. / Year: 1998 Title: An internal affinity-tag for purification and crystallization of the siderophore receptor FhuA, integral outer membrane protein from Escherichia coli K-12. Authors: Ferguson, A.D. / Breed, J. / Diederichs, K. / Welte, W. / Coulton, J.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qff.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qff.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qff_validation.pdf.gz | 665.6 KB | Display | wwPDB validaton report |
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Full document | 1qff_full_validation.pdf.gz | 695 KB | Display | |
Data in XML | 1qff_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 1qff_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qff ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qff | 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 80520.062 Da / Num. of mol.: 1 Mutation: SER-SER-HIS-HIS-HIS-HIS-HIS-HIS-GLY-SER-SER AFFINITY TAG Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH LIPOPOLYSACCHARIDE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Variant: RA CHEMOTYPE / Plasmid: PHX405 / Cellular location (production host): OUTER MEMBRANE / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 DL41 / References: UniProt: P06971 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-L-glycero- ...alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 9 types, 165 molecules
#3: Chemical | #4: Chemical | ChemComp-FTT / #5: Chemical | ChemComp-DAO / | #6: Chemical | ChemComp-MYR / | #7: Chemical | ChemComp-DPO / | #8: Chemical | ChemComp-EAP / | #9: Chemical | ChemComp-FCI / | #10: Chemical | #11: Water | ChemComp-HOH / | |
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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: 4.6 Å3/Da / Density % sol: 72.75 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 / Details: pH 6.4 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 290 K / 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: ESRF / Beamline: BM14 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1998 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→46.94 Å / Num. obs: 39663 / % possible obs: 98.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 60.4 Å2 / Rsym value: 0.079 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rsym value: 0.406 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 655667.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.82 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.032 / 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: 4.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 64.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.379 / % reflection Rfree: 2.3 % / Rfactor Rwork: 0.319 |