+Open data
-Basic information
Entry | Database: PDB / ID: 2zqk | ||||||
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Title | Crystal structure of intimin-Tir68 complex | ||||||
Components |
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Keywords | CELL ADHESION / protein-protein complex / unique intimin-Tir trimer intermediate / Cell membrane / Cell outer membrane / Membrane / Transmembrane / Virulence / Receptor | ||||||
Function / homology | Function and homology information cell outer membrane / cell adhesion / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ma, Y. / Gao, F. / Li, D.-F. / Gao, G.F. | ||||||
Citation | Journal: To be Published Title: Structural insight into the interaction between intimin and Tir of enterohaemorrhagic E coli: evidence for a dynamic sequential clustering-aggregating-reticulating model Authors: Ma, Y. / Zou, Q. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zqk.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zqk.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 2zqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/2zqk ftp://data.pdbj.org/pub/pdb/validation_reports/zq/2zqk | HTTPS FTP |
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-Related structure data
Related structure data | 2zwkC 1f02S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 20673.098 Da / Num. of mol.: 2 / Fragment: D2-D3 domain, UNP residues 747-934 Source method: isolated from a genetically manipulated source Details: inserted into NdeI and XhoI restrict enzyme sites / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: intimin adherence protein 747-934 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43261 #2: Protein | Mass: 8404.049 Da / Num. of mol.: 4 / Fragment: IBD domain, UNP residues 269-336 Source method: isolated from a genetically manipulated source Details: inserted into NdeI and XhoI restrict enzyme sites / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: Tir 269-336 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DB77 |
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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: 2.94 Å3/Da / Density % sol: 58.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1M HEPES sodium, 2% v/v PEG 400, 2.0M Ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 22064 / Num. obs: 20419 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 6.8 / Num. unique all: 1370 / Rsym value: 0.184 / % possible all: 65.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F02 Resolution: 2.8→34.1 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 20.79 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 163.62 Å2 / Biso mean: 75.428 Å2 / Biso min: 10.25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→34.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029
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