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- PDB-4phx: Crystal structure of AggB, the minor subunit of aggregative adher... -

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Basic information

Entry
Database: PDB / ID: 4phx
TitleCrystal structure of AggB, the minor subunit of aggregative adherence fimbriae type I from the Escherichia coli O4H104
ComponentsProtein AggB
KeywordsCELL ADHESION / Ig-like fold / beta sandwich / donor-strand complementation
Function / homologyEnterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Protein AggB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPakharukova, N.A. / Tuitilla, M. / Zavialov, A.V.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of FinlandFA-136333 Finland
Academy of FinlandFA-140959 Finland
Erasmus MundusTRIPLEI2011311 Finland
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
DepositionMay 7, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_data_processing_status ...diffrn_radiation_wavelength / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Dec 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein AggB
A: Protein AggB
C: Protein AggB
D: Protein AggB
E: Protein AggB
F: Protein AggB
G: Protein AggB
H: Protein AggB


Theoretical massNumber of molelcules
Total (without water)125,7348
Polymers125,7348
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-21 kcal/mol
Surface area49610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.797, 163.968, 58.627
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is a fimbriae made of polymerised of AggA subunits, and on the tip of the fimbriae minor subunit (AggB) is located. Assymmetric unit consists of eight AggB molecules

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Components

#1: Protein
Protein AggB


Mass: 15716.728 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aggB / Variant: AI / Plasmid: pET101D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P46006
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris HCl, pH 8.5, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→102.25 Å / Num. all: 50214 / Num. obs: 50214 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.069 / Rsym value: 0.062 / Net I/av σ(I): 7.452 / Net I/σ(I): 14.8 / Num. measured all: 261640
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.535.40.5652.83937472380.2620.5652.899.9
2.53-2.685.30.3642.13640268330.1710.3644.299.9
2.68-2.8750.2073.73225164420.1010.2076.6100
2.87-3.15.40.12363261960310.0570.12311.1100
3.1-3.395.40.0778.92968455450.0370.07717.1100
3.39-3.7950.059112504650440.0290.05921.899.9
3.79-4.385.30.05122403744980.0240.0527.899.9
4.38-5.3750.04413.41916738200.0220.04430.399.7
5.37-7.5950.04612.61502330020.0230.0462999.8
7.59-58.6274.60.04112.4803717610.0210.04130.999.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AXW

2axw


Resolution: 2.4→58.627 Å / FOM work R set: 0.7624 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 2542 5.07 %
Rwork0.2278 47600 -
obs0.23 50142 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.25 Å2 / Biso mean: 58.25 Å2 / Biso min: 21.58 Å2
Refinement stepCycle: final / Resolution: 2.4→58.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7935 0 0 312 8247
Biso mean---53.16 -
Num. residues----1028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098046
X-RAY DIFFRACTIONf_angle_d1.35210761
X-RAY DIFFRACTIONf_chiral_restr0.0871179
X-RAY DIFFRACTIONf_plane_restr0.0061377
X-RAY DIFFRACTIONf_dihedral_angle_d17.1712936
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.44620.36161510.271626242775100
2.4462-2.49610.34331520.273125472699100
2.4961-2.55040.33771440.274126332777100
2.5504-2.60970.35641430.263125832726100
2.6097-2.6750.3851320.279526332765100
2.675-2.74730.35011360.264525972733100
2.7473-2.82820.33331300.264226382768100
2.8282-2.91940.33061330.260626472780100
2.9194-3.02380.28541330.250326012734100
3.0238-3.14480.34161410.239426242765100
3.1448-3.2880.27031470.237926462793100
3.288-3.46130.3151330.226926422775100
3.4613-3.67810.28531340.224626592793100
3.6781-3.9620.25321510.210126402791100
3.962-4.36060.23341410.18626632804100
4.3606-4.99130.20471510.180526772828100
4.9913-6.28740.24911350.215527122847100
6.2874-58.64450.26611550.2652834298999

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