+Open data
-Basic information
Entry | Database: PDB / ID: 2gsk | |||||||||
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Title | Structure of the BtuB:TonB Complex | |||||||||
Components |
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Keywords | SIGNALING PROTEIN/MEMBRANE PROTEIN / OUTER-MEMBRANE ACTIVE TRANSPORT / BETA-BARREL / TONB / MEMBRANE PROTEIN / SIGNALING PROTEIN-MEMBRANE PROTEIN COMPLEX | |||||||||
Function / homology | Function and homology information receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / ABC-type vitamin B12 transporter activity / energy transducer activity / cell envelope / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / ABC-type vitamin B12 transporter activity / energy transducer activity / cell envelope / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / protein domain specific binding / calcium ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Shultis, D.D. / Purdy, M.P. / Banchs, C.N. / Wiener, M.C. | |||||||||
Citation | Journal: Science / Year: 2006 Title: Outer membrane active transport: structure of the BtuB:TonB complex Authors: Shultis, D.D. / Purdy, M.D. / Banchs, C.N. / Wiener, M.C. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and preliminary x-ray crystallographic analysis of the Escherichia coli outer membrane cobalamin transporter BtuB in complex with the carboxy-terminal domain of TonB Authors: Shultis, D.D. / Purdy, M.D. / Banchs, C.N. / Wiener, M.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gsk.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gsk.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gsk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gsk ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gsk | HTTPS FTP |
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-Related structure data
Related structure data | 1nqhS 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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Details | THE BIOLOGICAL ASSEMBLY IS A 1:1 COMPLEX OF BTUB AND TONB, WITH THE PHYSIOLOGICAL INTERFACE BETWEEN BTUB RESIDUES 6-12 AND TONB RESIDUES 158-171 AND 225-232. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 65954.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuB, bfe, cer, dcrC / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P06129 |
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#2: Protein | Mass: 9247.701 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tonB, exbA / Plasmid: PGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P94739, UniProt: P02929*PLUS |
-Non-polymers , 6 types, 286 molecules
#3: Chemical | #4: Chemical | ChemComp-CNC / | #5: Chemical | ChemComp-LDA / #6: Chemical | #7: Chemical | #8: 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: 2.5 Å3/Da / Density % sol: 50.75 % |
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Crystal grow | Temperature: 288 K / pH: 5.1 Details: 30% (v/v) PEG 300, 0.1M sodium acetate , pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 288K, pH 5.10 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.098→40 Å / Num. obs: 44005 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.436 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NQH Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.588 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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