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- PDB-7ko9: Crystal structure of antigen 43 from uropathogenic Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 7ko9
TitleCrystal structure of antigen 43 from uropathogenic Escherichia coli UTI89
ComponentsAidA-I family adhesin
KeywordsMICROBIAL PROTEIN / Autotransporters / Biofilm / Bacterial virulence / Bacterial infection
Function / homologyCITRIC ACID / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsVo, J.L. / Hor, L. / Paxman, J.J. / Heras, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)180102987 Australia
Australian Research Council (ARC)150102287 Australia
National Health and Medical Research Council (NHMRC, Australia)1143638 Australia
CitationJournal: NPJ Biofilms Microbiomes / Year: 2022
Title: Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms.
Authors: Vo, J.L. / Ortiz, G.C.M. / Totsika, M. / Lo, A.W. / Hancock, S.J. / Whitten, A.E. / Hor, L. / Peters, K.M. / Ageorges, V. / Caccia, N. / Desvaux, M. / Schembri, M.A. / Paxman, J.J. / Heras, B.
History
DepositionNov 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AidA-I family adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3079
Polymers56,5201
Non-polymers7878
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint11 kcal/mol
Surface area20890 Å2
Unit cell
Length a, b, c (Å)129.280, 132.820, 47.250
Angle α, β, γ (deg.)90.000, 94.130, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein AidA-I family adhesin / Antigen 43 / Autotransporter adhesin Ag43 / Autotransporter domain-containing protein / Putative ...Antigen 43 / Autotransporter adhesin Ag43 / Autotransporter domain-containing protein / Putative antigen 43 (Fluffing protein)


Mass: 56519.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: flu, AC789_1c11300, CT146_19135, EA231_25565, HmCmsJML146_03717, NCTC9434_03577
Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E1L650

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Non-polymers , 5 types, 205 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.2
Details: 20% 2-propanol, 100 mM trisodium citrate/citric acid pH 5.2, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.43→39.42 Å / Num. obs: 28779 / % possible obs: 96.3 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.054 / Rrim(I) all: 0.105 / Net I/σ(I): 9.9 / Num. measured all: 106281 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 % / % possible all: 96.1

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.43-2.520.6971129330080.7440.4160.8132
9.09-39.420.02621465720.9990.0160.0325.4

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Processing

Software
NameVersionClassification
Aimless0.3.5data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KH3

4kh3


Resolution: 2.43→39.42 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 1325 4.61 %
Rwork0.1646 27434 -
obs0.1666 28759 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.09 Å2 / Biso mean: 50.0801 Å2 / Biso min: 26.88 Å2
Refinement stepCycle: final / Resolution: 2.43→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 52 197 4079
Biso mean--65.04 49.97 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073913
X-RAY DIFFRACTIONf_angle_d0.9275309
X-RAY DIFFRACTIONf_dihedral_angle_d11.035578
X-RAY DIFFRACTIONf_chiral_restr0.06621
X-RAY DIFFRACTIONf_plane_restr0.005714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.530.27081300.25223039316996
2.53-2.640.30881600.23863026318696
2.64-2.780.24971710.21373024319596
2.78-2.960.27431380.19483062320096
2.96-3.180.25041340.1753066320097
3.18-3.50.20281640.16473039320397
3.5-4.010.18451380.1423054319296
4.01-5.050.15111450.12193052319796
5.05-39.420.20351450.16353072321795
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.68920.18651.8420.9930.0773.92550.1512-0.943-0.13220.2385-0.1189-0.04950.31760.4878-0.05890.417-0.00280.02120.84140.04570.2846177.7896-16.5086126.5372
25.27350.45753.25560.90590.99083.2052-0.097-0.13260.06190.0376-0.03380.1418-0.01850.16480.07750.2924-0.05030.01920.26060.00950.2786153.6906-15.1988105.6928
31.59050.85441.03823.17722.19033.433-0.0801-0.00720.1654-0.1237-0.07950.0001-0.1799-0.01310.19390.23470.0021-0.00230.26880.03750.3171135.197-24.885883.3709
42.7354-1.52550.45116.92770.81621.92560.14510.1572-0.317-0.2742-0.0034-0.33320.21880.3209-0.11730.3310.08690.05760.3791-0.02960.3203140.0339-50.403365.9441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 142 )A2 - 142
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 276 )A143 - 276
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 416 )A277 - 416
4X-RAY DIFFRACTION4chain 'A' and (resid 417 through 561 )A417 - 561

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