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- PDB-1f00: CRYSTAL STRUCTURE OF C-TERMINAL 282-RESIDUE FRAGMENT OF ENTEROPAT... -

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Basic information

Entry
Database: PDB / ID: 1f00
TitleCRYSTAL STRUCTURE OF C-TERMINAL 282-RESIDUE FRAGMENT OF ENTEROPATHOGENIC E. COLI INTIMIN
ComponentsINTIMIN
KeywordsCELL ADHESION / Immunoglobulin-like fold / C-type lectin-like fold
Function / homology
Function and homology information


peptidoglycan binding / cell outer membrane / cell adhesion / protein homodimerization activity / identical protein binding
Similarity search - Function
Intimin, C-terminal / Intimin C-type lectin domain / NUP210 Ig-like domain 5 / 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) ...Intimin, C-terminal / Intimin C-type lectin domain / NUP210 Ig-like domain 5 / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 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 12, 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 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: INTIMIN


Theoretical massNumber of molelcules
Total (without water)30,0851
Polymers30,0851
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.160, 47.100, 71.660
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.8 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal grow
*PLUS
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: Jan 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 27521 / Num. obs: 24955 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.73 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.261 / Num. unique all: 875 / % possible all: 51.5
Reflection shell
*PLUS
% possible obs: 51.5 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2440 -RANDOM
Rwork0.215 ---
all0.215 27521 --
obs0.215 24543 90.7 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 0 190 2304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.051
X-RAY DIFFRACTIONc_angle_deg1.419

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