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Yorodumi- PDB-2grx: Crystal structure of TonB in complex with FhuA, E. coli outer mem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2grx | |||||||||
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Title | Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for ferrichrome | |||||||||
Components |
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Keywords | METAL TRANSPORT / BETA BARREL / OUTER MEMBRANE / HETEROCOMPLEX / INTER-PROTEIN BETA SHEET / PROTEIN-PROTEIN | |||||||||
Function / homology | Function and homology information receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / cell envelope / siderophore transmembrane transport / cobalamin transport / siderophore transport / siderophore uptake transmembrane transporter activity / intracellular monoatomic cation homeostasis / plasma membrane protein complex ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / cell envelope / siderophore transmembrane transport / cobalamin transport / siderophore transport / siderophore uptake transmembrane transporter activity / intracellular monoatomic cation homeostasis / plasma membrane protein complex / virion binding / toxic substance binding / transmembrane transporter complex / cell outer membrane / transmembrane transport / protein transport / signaling receptor activity / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / iron ion binding / protein domain specific binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Pawelek, P.D. / Allaire, M. / Coulton, J.W. | |||||||||
Citation | Journal: Science / Year: 2006 Title: Structure of TonB in complex with FhuA, E. coli outer membrane receptor. Authors: Pawelek, P.D. / Croteau, N. / Ng-Thow-Hing, C. / Khursigara, C.M. / Moiseeva, N. / Allaire, M. / 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 | 2grx.cif.gz | 300.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2grx.ent.gz | 242.3 KB | Display | PDB format |
PDBx/mmJSON format | 2grx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2grx_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 2grx_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 2grx_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 2grx_validation.cif.gz | 89.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/2grx ftp://data.pdbj.org/pub/pdb/validation_reports/gr/2grx | HTTPS FTP |
-Related structure data
Related structure data | 1fcpS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 80051.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fhuA / Production host: Escherichia coli (E. coli) / Strain (production host): AW740 / References: UniProt: P06971 #2: Protein | Mass: 24973.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tonB / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P94739, UniProt: P02929*PLUS |
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-Sugars , 1 types, 2 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 7 types, 19 molecules
#4: Chemical | #5: Chemical | ChemComp-FTT / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-MYR / | |
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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: 3.1 Å3/Da / Density % sol: 60.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 8% polyethylene glycol 4000, 50 mM MES (pH 6.0), 75 mM NaCl, 5% glycerol, 0.7% C8E4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.932 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 39013 / Num. obs: 38697 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 68.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.3→3.51 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5883 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FCP Resolution: 3.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 25.447 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.023
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Xplor file |
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