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Yorodumi- PDB-4cu4: FhuA from E. coli in complex with the lasso peptide microcin J25 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cu4 | |||||||||
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Title | FhuA from E. coli in complex with the lasso peptide microcin J25 (MccJ25) | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN/ANTIBIOTIC / TRANSPORT PROTEIN-ANTIBIOTIC COMPLEX / LIPOPOLYSACCHARIDE / DETERGENT | |||||||||
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 / killing of cells of another organism / defense response to bacterium ...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 / killing of cells of another organism / defense response to bacterium / iron ion binding / protein domain specific binding / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria) ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Mathavan, I. / Rebuffat, S. / Beis, K. | |||||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2014 Title: Structural Basis for Hijacking Siderophore Receptors by Antimicrobial Lasso Peptides. Authors: Mathavan, I. / Zirah, S. / Mehmood, S. / Choudhury, H.G. / Goulard, C. / Li, Y. / Robinson, C.V. / Rebuffat, S. / Beis, K. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cu4.cif.gz | 176.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cu4.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 4cu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cu4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4cu4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4cu4_validation.xml.gz | 33 KB | Display | |
Data in CIF | 4cu4_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/4cu4 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/4cu4 | HTTPS FTP |
-Related structure data
Related structure data | 2fcpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB
#1: Protein | Mass: 78100.961 Da / Num. of mol.: 1 / Fragment: RESIDUES 53-747 Source method: isolated from a genetically manipulated source Details: HIS-TAG BETWEEN RESIDUE P405 AND V417. SEQUENCE INSERTED SSHHHHHHGSS Source: (gene. exp.) ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria) Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P06971 |
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#2: Protein/peptide | |
#3: Polysaccharide | L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy- ...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-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 8 types, 199 molecules
#4: Chemical | ChemComp-FTT / #5: Chemical | ChemComp-DAO / | #6: Chemical | ChemComp-MYR / | #7: Chemical | ChemComp-LDA / #8: Chemical | ChemComp-3PH / | #9: Chemical | #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Details
Sequence details | INTRODUCED |
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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: 4.44 Å3/Da / Density % sol: 72.3 % / Description: NONE |
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Crystal grow | pH: 5 Details: 20 MM TRIS PH 7.5, 120 MM LITHIUM SULFATE, 100 MM SODIUM CITRATE PH 5, 20 % PEG300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30.46 Å / Num. obs: 62620 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FCP Resolution: 2.3→30.46 Å / Cor.coef. Fo:Fc: 0.8875 / Cor.coef. Fo:Fc free: 0.8605 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.186 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. THE ELECTRON DENSITY AT THE INTERNAL HIS-TAG LOOP REGION WAS TOO WEAK TO ALLOW BUILDING RESIDUES 405-417 RELIABLY
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Displacement parameters | Biso mean: 56.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.348 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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