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- PDB-6k73: Chaperone-tip adhesin complex is vital for synergistic activation... -

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Basic information

Entry
Database: PDB / ID: 6k73
TitleChaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis
Components
  • CFA/I fimbrial subunit E
  • Colonization factor antigen I chaperone CfaA
KeywordsCHAPERONE / Enterotoxigenic Escherichia coli / chaperone-usher fimbriae / periplasmic chaperone / adhesive subunit / binding motif
Function / homology
Function and homology information


Immunoglobulin-like - #3970 / CblD-like pilus biogenesis initiator / CFA/I fimbrial subunit E, adhesin domain / CblD like pilus biogenesis initiator / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / : / CfA/I fimbrial subunit A (Colonization factor antigen subunit A putative chaperone) / CFA/I fimbrial subunit E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7742 Å
AuthorsBao, R. / He, L.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)SQ2016YFJC040104 China
CitationJournal: Plos Pathog. / Year: 2020
Title: Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis.
Authors: He, L.H. / Wang, H. / Liu, Y. / Kang, M. / Li, T. / Li, C.C. / Tong, A.P. / Zhu, Y.B. / Song, Y.J. / Savarino, S.J. / Prouty, M.G. / Xia, D. / Bao, R.
History
DepositionJun 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Colonization factor antigen I chaperone CfaA
B: Colonization factor antigen I chaperone CfaA
C: CFA/I fimbrial subunit E
D: CFA/I fimbrial subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,88012
Polymers126,2774
Non-polymers6038
Water82946
1
A: Colonization factor antigen I chaperone CfaA
C: CFA/I fimbrial subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6839
Polymers63,1392
Non-polymers5447
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-32 kcal/mol
Surface area25990 Å2
MethodPISA
2
B: Colonization factor antigen I chaperone CfaA
D: CFA/I fimbrial subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1973
Polymers63,1392
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-29 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.158, 217.158, 177.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-405-

NI

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Components

#1: Protein Colonization factor antigen I chaperone CfaA


Mass: 25263.092 Da / Num. of mol.: 2 / Mutation: T112I,L114I,V116I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: D4V05_24280 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3Y5Z8F9, UniProt: E3PPC3*PLUS
#2: Protein CFA/I fimbrial subunit E / Colonization factor antigen I subunit E


Mass: 37875.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cfaE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25734
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2%PEG8000, 0.1M imidazole malate, 1.04M Li2SO4, 0.01M GSSG-GSH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.774→30 Å / Num. obs: 40388 / % possible obs: 99.69 % / Observed criterion σ(I): 3.6 / Redundancy: 7.5 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 12.29
Reflection shellResolution: 2.774→2.87 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.562 / Num. unique obs: 10 / Rsym value: 0.562 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHENIXmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7742→29.5168 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2597 --
Rwork0.2248 --
obs0.2265 40387 99.54 %
Refinement stepCycle: LAST / Resolution: 2.7742→29.5168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8358 0 28 46 8432

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