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- PDB-1f02: CRYSTAL STRUCTURE OF C-TERMINAL 282-RESIDUE FRAGMENT OF INTIMIN I... -

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Basic information

Entry
Database: PDB / ID: 1f02
TitleCRYSTAL STRUCTURE OF C-TERMINAL 282-RESIDUE FRAGMENT OF INTIMIN IN COMPLEX WITH TRANSLOCATED INTIMIN RECEPTOR (TIR) INTIMIN-BINDING DOMAIN
Components
  • INTIMIN
  • TRANSLOCATED INTIMIN RECEPTOR
KeywordsCELL ADHESION / Immunoglobulin-like fold / C-type lectin-like fold / four-helix bundle
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 / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / : / Inverse autotransporter, beta-domain / Immunoglobulin-like - #1080 / Bacterial Ig-like domain (group 1) / 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 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 / Immunoglobulins / 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 / Resolution: 2.9 Å
AuthorsLuo, Y. / Frey, E.A. / Pfuetzner, R.A. / Creagh, A.L. / Knoechel, D.G. / Haynes, C.A. / Finlay, B.B. / Strynadka, N.C.J.
CitationJournal: Nature / Year: 2000
Title: Crystal structure of enteropathogenic Escherichia coli intimin-receptor complex.
Authors: Luo, Y. / Frey, E.A. / Pfuetzner, R.A. / Creagh, A.L. / Knoechel, D.G. / Haynes, C.A. / Finlay, B.B. / Strynadka, N.C.
History
DepositionMay 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
I: INTIMIN
T: TRANSLOCATED INTIMIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)37,1432
Polymers37,1432
Non-polymers00
Water00
1
T: TRANSLOCATED INTIMIN RECEPTOR

I: INTIMIN
T: TRANSLOCATED INTIMIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)44,2023
Polymers44,2023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation4_554x,-y,-z-11
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.500, 349.000, 47.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein INTIMIN


Mass: 30084.533 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (282 RESIDUES)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19809
#2: Protein TRANSLOCATED INTIMIN RECEPTOR / TIR


Mass: 7058.585 Da / Num. of mol.: 1 / Fragment: INTIMIN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KWH9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8 M ammonium sulphate, 200 mM Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
Conc.: 1.8 M / Details: or 2.5M ammonium sulfate / Chemical formula: K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 17457 / Num. obs: 16811 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.08 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.2
Reflection shellResolution: 2.9→2.96 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.283 / Num. unique all: 821 / % possible all: 74.9
Reflection shell
*PLUS
% possible obs: 74.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1578 -RANDOM
Rwork0.247 ---
all0.247 17457 --
obs0.247 15850 90.8 %-
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 0 0 2608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.391

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