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- PDB-4or1: Structure and mechanism of fibronectin binding and biofilm format... -

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Basic information

Entry
Database: PDB / ID: 4or1
TitleStructure and mechanism of fibronectin binding and biofilm formation of enteroaggregative Escherischia coli AAF fimbriae
ComponentsInvasin homolog AafB, Major fimbrial subunit of aggregative adherence fimbria II AafA chimeric construct
KeywordsCELL ADHESION / biofilm / chaperone-usher / pilus / adhesion / fibronectin / fimbriae / fibre / immunoglobulin-like / Outer membrane pilus
Function / homology
Function and homology information


Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Dr adhesin / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Major fimbrial subunit of aggregative adherence fimbria II AafA / Invasin homolog AafB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, W.-C. / Garnett, J.A. / Yang, Y. / Matthews, S.
CitationJournal: Plos Pathog. / Year: 2014
Title: Structural insight into host recognition by aggregative adherence fimbriae of enteroaggregative Escherichia coli.
Authors: Berry, A.A. / Yang, Y. / Pakharukova, N. / Garnett, J.A. / Lee, W.C. / Cota, E. / Marchant, J. / Roy, S. / Tuittila, M. / Liu, B. / Inman, K.G. / Ruiz-Perez, F. / Mandomando, I. / Nataro, J. ...Authors: Berry, A.A. / Yang, Y. / Pakharukova, N. / Garnett, J.A. / Lee, W.C. / Cota, E. / Marchant, J. / Roy, S. / Tuittila, M. / Liu, B. / Inman, K.G. / Ruiz-Perez, F. / Mandomando, I. / Nataro, J.P. / Zavialov, A.V. / Matthews, S.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Invasin homolog AafB, Major fimbrial subunit of aggregative adherence fimbria II AafA chimeric construct
B: Invasin homolog AafB, Major fimbrial subunit of aggregative adherence fimbria II AafA chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5274
Polymers34,3722
Non-polymers1552
Water362
1
A: Invasin homolog AafB, Major fimbrial subunit of aggregative adherence fimbria II AafA chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2822
Polymers17,1861
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Invasin homolog AafB, Major fimbrial subunit of aggregative adherence fimbria II AafA chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2452
Polymers17,1861
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.755, 81.755, 222.703
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Invasin homolog AafB, Major fimbrial subunit of aggregative adherence fimbria II AafA chimeric construct


Mass: 17186.150 Da / Num. of mol.: 2
Fragment: AAF/II pilus minor pilin, unp residues 24-146 and unp residues 25-34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Enteroaggregative 042 / Gene: aafB, aafA / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q9X4L4, UniProt: O30595
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BIS-TRIS, 0.2 M LiSO4, 25% PEG3350., pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3→51.24 Å / Num. all: 9081 / Num. obs: 9081 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 74.4 Å2 / Rsym value: 0.111 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1302 / Rsym value: 0.374 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0062refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AXW

2axw


Resolution: 3→51.24 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.549 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.995 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 437 4.8 %RANDOM
Rwork0.22017 ---
obs0.22149 8638 95.77 %-
all-8638 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 3→51.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 9 2 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211959
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9332650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66423.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.981512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021468
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 34 -
Rwork0.315 619 -
obs--96.74 %

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