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- PDB-2hdi: Crystal structure of the Colicin I receptor Cir from E.coli in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hdi | ||||||
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Title | Crystal structure of the Colicin I receptor Cir from E.coli in complex with receptor binding domain of Colicin Ia. | ||||||
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![]() | Protein Transport / Antimicrobial Protein / Outer membrane / Iron transport / TonB box / Signal transduction / Colicin I Receptor / Receptor Ligand / Membrane Protein | ||||||
Function / homology | ![]() siderophore-iron transmembrane transporter activity / pore-forming activity / colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / killing of cells of another organism ...siderophore-iron transmembrane transporter activity / pore-forming activity / colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / killing of cells of another organism / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Buchanan, S.K. / Esser, L. / Lukacik, P. | ||||||
![]() | ![]() Title: Structure of colicin I receptor bound to the R-domain of colicin Ia: implications for protein import. Authors: Buchanan, S.K. / Lukacik, P. / Grizot, S. / Ghirlando, R. / Ali, M.M. / Barnard, T.J. / Jakes, K.S. / Kienker, P.K. / Esser, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.6 KB | Display | ![]() |
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PDB format | ![]() | 123.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2hdfSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 71294.242 Da / Num. of mol.: 1 / Fragment: Colicin I receptor / Mutation: W338M, L343M, F589M, V591M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 12891.374 Da / Num. of mol.: 1 / Fragment: R domain of Colicin Ia Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.62 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 9 G/L PROTEIN IN 0.02M TRIS PH7.5, 0.2M NACL, 0.05% LDAO, 0.45% C8E4, 3% HEPTANETRIOL MIXED AT 1:1 RATIO WITH 0.1M MES PH6.2, 10% GLYCEROL, 22% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2004 |
Radiation | Monochromator: Si 220 (Rosenbaum-Rock double-crystal monochromator) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 32311 / Num. obs: 32311 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.73 / Num. unique all: 3632 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HDF Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.389 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.48 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.563 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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