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- PDB-2zqk: Crystal structure of intimin-Tir68 complex -

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Basic information

Entry
Database: PDB / ID: 2zqk
TitleCrystal structure of intimin-Tir68 complex
Components
  • Intimin
  • Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
KeywordsCELL 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
Translocated Intimin Receptor; Chain T / Translocated intimin receptor, central domain / Translocated intimin receptor, central domain / Translocated intimin receptor, N-terminal / Translocated intimin receptor / Translocated intimin receptor, C-terminal / Translocated intimin receptor, central domain superfamily / Translocated intimin receptor (Tir) intimin-binding domain / Translocated intimin receptor (Tir) C-terminus / Translocated intimin receptor (Tir) N-terminus ...Translocated Intimin Receptor; Chain T / Translocated intimin receptor, central domain / Translocated intimin receptor, central domain / Translocated intimin receptor, N-terminal / Translocated intimin receptor / Translocated intimin receptor, C-terminal / Translocated intimin receptor, central domain superfamily / Translocated intimin receptor (Tir) intimin-binding domain / Translocated intimin receptor (Tir) C-terminus / Translocated intimin receptor (Tir) N-terminus / Intimin, C-terminal / Intimin C-type lectin domain / Immunoglobulin-like - #1080 / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / Bacterial Ig-like domain (group 1) / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / C-type lectin fold / Few Secondary Structures / Irregular / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Intimin / Translocated intimin receptor Tir
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMa, Y. / Gao, F. / Li, D.-F. / Gao, G.F.
CitationJournal: 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
DepositionAug 12, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intimin
M: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
N: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
B: Intimin
C: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
D: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


Theoretical massNumber of molelcules
Total (without water)74,9626
Polymers74,9626
Non-polymers00
Water0
1
A: Intimin
M: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
N: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


Theoretical massNumber of molelcules
Total (without water)37,4813
Polymers37,4813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intimin
C: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
D: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


Theoretical massNumber of molelcules
Total (without water)37,4813
Polymers37,4813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Intimin


Theoretical massNumber of molelcules
Total (without water)20,6731
Polymers20,6731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Intimin


Theoretical massNumber of molelcules
Total (without water)20,6731
Polymers20,6731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
M: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
N: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


Theoretical massNumber of molelcules
Total (without water)16,8082
Polymers16,8082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10 kcal/mol
Surface area8040 Å2
MethodPISA
6
C: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
D: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


Theoretical massNumber of molelcules
Total (without water)16,8082
Polymers16,8082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-9 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.680, 42.310, 182.080
Angle α, β, γ (deg.)90.00, 101.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Intimin / / Attaching and effacing protein / Eae protein / Gamma-intimin


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
Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F02

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
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1973 -RANDOM
Rwork0.241 ---
obs0.241 20136 91.3 %-
all-22064 --
Solvent computationBsol: 20.79 Å2
Displacement parametersBiso max: 163.62 Å2 / Biso mean: 75.428 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.903 Å20 Å2-11.944 Å2
2--41.003 Å20 Å2
3----41.906 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 0 0 4739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.376
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.416 212 -
Rwork0.382 --
obs-2196 66.4 %

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