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- PDB-4ph8: Crystal structure of AggA, the major subunit of aggregative adher... -

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Basic information

Entry
Database: PDB / ID: 4ph8
TitleCrystal structure of AggA, the major subunit of aggregative adherence fimbriae type I (AAF/I) from the Escherichia coli O4H104
ComponentsAggregative adherence fimbrial subunit AggA
KeywordsCELL ADHESION / Beta sandwich / donor-strand complementation / fibronectin binding
Function / homologyImmunoglobulin-like - #2910 / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesEscherichia coli O104:H4 str. C227-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
Model detailsstructure is linked with 4OR1
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 MumdusTRIPLEI2011311 Finland
Citation
Journal: 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.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization and sulfur SAD phasing of AggA, the major subunit of aggregative adherence fimbriae type I from the Escherichia coli strain that caused an outbreak of haemolytic-uraemic syndrome in Germany.
Authors: Pakharukova, N. / Tuittila, M. / Zavialov, A.
History
DepositionMay 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
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
A: Aggregative adherence fimbrial subunit AggA
B: Aggregative adherence fimbrial subunit AggA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7224
Polymers33,5382
Non-polymers1842
Water5,314295
1
A: Aggregative adherence fimbrial subunit AggA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8612
Polymers16,7691
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aggregative adherence fimbrial subunit AggA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8612
Polymers16,7691
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.832, 80.172, 91.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
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 two AggA subunits

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Components

#1: Protein Aggregative adherence fimbrial subunit AggA / Aggregative adherence fimbriae / type I (AAF/I) / major subunit / AggA / Shiga-toxin producing E.coli


Mass: 16768.891 Da / Num. of mol.: 2 / Fragment: Residues 41-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O104:H4 str. C227-11 (bacteria)
Gene: EUAG_05069 / Plasmid: pET101D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: G5TBZ9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.22 Å3/Da / Density % sol: 44.56 % / Description: Single crystal, dimensions 0.6 mm x 0.2 mm
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium acetate, 0.1M sodium cacodylate, 30% w/v PEG 8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.954
SYNCHROTRONESRF BM1421.75
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 11, 2012
MARMOSAIC 225 mm CCD2CCDOct 11, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
21.751
ReflectionResolution: 1.55→91.416 Å / Num. all: 40475 / Num. obs: 40475 / % possible obs: 97.2 % / Redundancy: 4.2 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.044 / Rsym value: 0.038 / Net I/av σ(I): 14.273 / Net I/σ(I): 19 / Num. measured all: 170118
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
1.55-1.634.30.78712473757580.4270.7872.195.8
1.63-1.734.30.4721.62352854840.2560.4723.396.4
1.73-1.854.30.26232225351990.1430.2625.796.7
1.85-24.30.1186.52073248600.0640.11811.197.2
2-2.194.20.06711.51901344950.0370.06718.397.7
2.19-2.454.20.04915.51725841050.0270.04923.798.1
2.45-2.834.10.03520.11516636660.0190.03532.198.5
2.83-3.474.10.02624.61264831170.0140.02646.298.7
3.47-4.940.01933.3967324400.0110.0195798.8
4.9-47.6563.80.01639.3511013510.0090.0165595.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
REFMAC5.8.0071refinement
PHASERphasing
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.55→55.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2224 / WRfactor Rwork: 0.1503 / FOM work R set: 0.8261 / SU B: 4.706 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1125 / SU Rfree: 0.1005 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 1854 4.9 %RANDOM
Rwork0.1562 36021 --
obs0.1598 37875 90.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.87 Å2 / Biso mean: 24.834 Å2 / Biso min: 8.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.04 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.55→55.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 12 295 2549
Biso mean--36.87 36.96 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192308
X-RAY DIFFRACTIONr_bond_other_d0.0010.022209
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9363155
X-RAY DIFFRACTIONr_angle_other_deg0.73135096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.88225.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7515367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.754152
X-RAY DIFFRACTIONr_chiral_restr0.0750.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
X-RAY DIFFRACTIONr_mcbond_it3.052.221200
X-RAY DIFFRACTIONr_mcbond_other3.0532.2181199
X-RAY DIFFRACTIONr_mcangle_it3.8763.3331497
X-RAY DIFFRACTIONr_rigid_bond_restr1.91734513
X-RAY DIFFRACTIONr_sphericity_free36.2725100
X-RAY DIFFRACTIONr_sphericity_bonded14.40454662
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 107 -
Rwork0.26 2205 -
all-2312 -
obs--76.53 %

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