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- PDB-4kh3: Structure of a bacterial self-associating protein -

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Basic information

Entry
Database: PDB / ID: 4kh3
TitleStructure of a bacterial self-associating protein
ComponentsAntigen 43
KeywordsIMMUNE SYSTEM / Self-associating protein / Uropathogenic Escherichia coli / AIDA-I type autotransporter / Ag43 / aggregation / biofilm
Function / homology
Function and homology information


Adhesin of bacterial autotransporter system / Adhesin of bacterial autotransporter system, probable stalk / Pectate Lyase C-like - #20 / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily ...Adhesin of bacterial autotransporter system / Adhesin of bacterial autotransporter system, probable stalk / Pectate Lyase C-like - #20 / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
MALONATE ION / Antigen 43 / Antigen 43
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsHeras, B. / Gee, C.L. / Schembri, M.A. / Totsika, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping.
Authors: Heras, B. / Totsika, M. / Peters, K.M. / Paxman, J.J. / Gee, C.L. / Jarrott, R.J. / Perugini, M.A. / Whitten, A.E. / Schembri, M.A.
History
DepositionApr 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Derived calculations
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Antigen 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8848
Polymers50,1691
Non-polymers7147
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.045, 106.045, 147.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-768-

HOH

21A-778-

HOH

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Components

#1: Protein Antigen 43 /


Mass: 50169.238 Da / Num. of mol.: 1 / Fragment: alpha domain, UNP RESIDUES 55-554
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: agn43, c3655 / Plasmid: pETLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q8CVR0, UniProt: A0A0H2VAW5*PLUS
#2: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4
Details: 2.8M sodium malonate pH 4, 10mM ATP, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX110.954383
SYNCHROTRONAustralian Synchrotron MX120.953663
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 210r1CCDAug 1, 2009mirrors
ADSC QUANTUM 210r2CCDApr 14, 2010mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Si with sagittaly bent second crystalSINGLE WAVELENGTHMx-ray1
2Double Si with sagittaly bent second crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9543831
20.9536631
ReflectionResolution: 2.5→19.7 Å / Num. all: 29768 / Num. obs: 29768 / % possible obs: 99.8 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.124
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 4.6 / Num. unique all: 4278 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceGUI interface to EPICS controldata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.692 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 2784 9.36 %RANDOM
Rwork0.1676 ---
all0.1721 29742 --
obs0.1721 29742 99.94 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.679 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3801 Å2-0 Å20 Å2
2--0.3801 Å2-0 Å2
3----0.7601 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 49 306 3800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073568
X-RAY DIFFRACTIONf_angle_d1.0044846
X-RAY DIFFRACTIONf_dihedral_angle_d14.2211241
X-RAY DIFFRACTIONf_chiral_restr0.065580
X-RAY DIFFRACTIONf_plane_restr0.003659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.54310.32551400.2538131899
2.5431-2.58920.33241320.25741322100
2.5892-2.63890.31791300.21871332100
2.6389-2.69260.27161320.2051324100
2.6926-2.7510.27021350.19461317100
2.751-2.81490.22261350.19221322100
2.8149-2.8850.25491410.17161343100
2.885-2.96280.24411380.17391324100
2.9628-3.04970.24041410.16241320100
3.0497-3.14770.19631380.16641328100
3.1477-3.25970.21761370.1591339100
3.2597-3.38960.19651380.16091341100
3.3896-3.54310.2351410.16881341100
3.5431-3.72870.20231390.151342100
3.7287-3.96050.19821400.15811356100
3.9605-4.26340.17411410.13591353100
4.2634-4.68720.14921420.11321369100
4.6872-5.35350.18451440.13621380100
5.3535-6.70050.21621450.18681405100
6.7005-19.69270.23271550.22031482100

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