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- PDB-2zwk: Crystal structure of intimin-Tir90 complex -

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Basic information

Entry
Database: PDB / ID: 2zwk
TitleCrystal structure of intimin-Tir90 complex
Components
  • Intimin
  • Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
KeywordsCELL ADHESION / protein-protein complex / unique intimin-Tir octamer 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: 3.1 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
DepositionDec 16, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 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
B: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
C: Intimin
D: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
E: Intimin
F: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


Theoretical massNumber of molelcules
Total (without water)84,4816
Polymers84,4816
Non-polymers00
Water0
1
A: Intimin
B: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)

A: Intimin
B: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)

A: Intimin
B: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)

A: Intimin
B: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


Theoretical massNumber of molelcules
Total (without water)112,6418
Polymers112,6418
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_645-x+1,-y-1,z1
crystal symmetry operation15_645y+1,x-1,-z1
2
C: Intimin
D: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
E: Intimin
F: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)

C: Intimin
D: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)
E: Intimin
F: Putative translocated intimin receptor protein (Translocated intimin receptor Tir)


Theoretical massNumber of molelcules
Total (without water)112,6418
Polymers112,6418
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Unit cell
Length a, b, c (Å)96.780, 96.780, 644.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 20171.564 Da / Num. of mol.: 3 / Fragment: D2-D3 domain, UNP residues 752-934
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: intimin / 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: 7988.650 Da / Num. of mol.: 3 / Fragment: IBD domain, UNP residues 274-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: tir / 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: 4.46 Å3/Da / Density % sol: 72.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M (NH4)2SO4, 5% 2-Propanol, pH 4.6, 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-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→66.67 Å / Num. all: 28764 / Num. obs: 26817 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 11.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3900 / Rsym value: 0.413 / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZQK

2zqk


Resolution: 3.1→66.67 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.36 2344 -RANDOM
Rwork0.301 ---
all0.301 28764 --
obs-23899 83.1 %-
Solvent computationBsol: 97.151 Å2
Displacement parametersBiso max: 202.14 Å2 / Biso mean: 115 Å2 / Biso min: 42.53 Å2
Baniso -1Baniso -2Baniso -3
1-39.711 Å20 Å20 Å2
2--39.711 Å20 Å2
3----79.422 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.65 Å
Luzzati d res low-5 Å
Luzzati sigma a1 Å1 Å
Refinement stepCycle: LAST / Resolution: 3.1→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5655 0 0 0 5655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 3.1→3.29 Å
RfactorNum. reflection% reflection
Rfree0.526 337 -
Rwork0.536 --
obs-3193 75.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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