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- PDB-6fqa: Crystal structure of the CsuC-CsuA/B chaperone-subunit preassembl... -

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Basic information

Entry
Database: PDB / ID: 6fqa
TitleCrystal structure of the CsuC-CsuA/B chaperone-subunit preassembly complex of the archaic chaperone-usher Csu pili of Acinetobacter baumannii
Components
  • CsuA/B,CsuA/B
  • CsuC
KeywordsCELL ADHESION / Ig-like fold / beta sandwich / donor-strand complementation
Function / homology
Function and homology information


cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Spore coat protein U / Spore Coat Protein U domain / Spore Coat Protein U domain / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsParilova, O. / Pakharukova, N.A. / Malmi, H. / Tuitilla, M. / Paavilainen, S. / Zavialov, A.V.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland273075 Finland
Juselius Foundation Finland
Magnus Ehrnrooth foundation Finland
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Archaic and alternative chaperones preserve pilin folding energy by providing incomplete structural information.
Authors: Pakharukova, N. / McKenna, S. / Tuittila, M. / Paavilainen, S. / Malmi, H. / Xu, Y. / Parilova, O. / Matthews, S. / Zavialov, A.V.
History
DepositionFeb 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CsuC
B: CsuA/B,CsuA/B
C: CsuC
D: CsuA/B,CsuA/B


Theoretical massNumber of molelcules
Total (without water)85,8704
Polymers85,8704
Non-polymers00
Water00
1
A: CsuC
B: CsuA/B,CsuA/B


Theoretical massNumber of molelcules
Total (without water)42,9352
Polymers42,9352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-16 kcal/mol
Surface area17020 Å2
MethodPISA
2
C: CsuC
D: CsuA/B,CsuA/B


Theoretical massNumber of molelcules
Total (without water)42,9352
Polymers42,9352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-16 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.379, 94.379, 390.745
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 8 through 33 or resid 35...
21(chain D and (resid 8 through 18 or resid 29...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resid 8 through 33 or resid 35...B8 - 33
121(chain B and (resid 8 through 33 or resid 35...B35 - 49
131(chain B and (resid 8 through 33 or resid 35...B55 - 85
141(chain B and (resid 8 through 33 or resid 35...B89 - 132
151(chain B and (resid 8 through 33 or resid 35...B136 - 152
211(chain D and (resid 8 through 18 or resid 29...D8 - 18
221(chain D and (resid 8 through 18 or resid 29...D29 - 33
231(chain D and (resid 8 through 18 or resid 29...D35 - 129
241(chain D and (resid 8 through 18 or resid 29...D132
251(chain D and (resid 8 through 18 or resid 29...D136 - 138
261(chain D and (resid 8 through 18 or resid 29...D140 - 152

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Components

#1: Protein CsuC


Mass: 27004.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: csuC / Plasmid: pET101 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q6XBY4
#2: Protein CsuA/B,CsuA/B


Mass: 15930.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: csuA/B / Plasmid: pET101 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q6XBY7

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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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium malonate, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.85→390.745 Å / Num. all: 24880 / Num. obs: 24880 / % possible obs: 99.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 56.29 Å2 / Rpim(I) all: 0.058 / Rrim(I) all: 0.167 / Rsym value: 0.157 / Net I/av σ(I): 4.6 / Net I/σ(I): 11.3 / Num. measured all: 195696
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.85-36.40.8660.92267235460.3640.9430.866299.5
3-3.198.50.5991.32859033710.2150.6380.5993.799.6
3.19-3.418.30.4111.82648331860.1490.4380.4115.499.5
3.41-3.688.10.24432391929610.0890.2610.2448.599.5
3.68-4.038.40.1784.22292327360.0640.1890.17811.499.2
4.03-4.517.90.1066.71994825140.0390.1140.10616.599.1
4.51-5.28.20.0818.81830422210.0290.0870.08121.198.9
5.2-6.377.80.0957.71481419080.0350.1010.0951898.7
6.37-9.017.60.071101154615110.0270.0760.0712298.3
9.01-46.84970.0414.764979260.0150.0430.0435.797.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FQ0

6fq0


Resolution: 2.85→47.189 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 1310 5.27 %
Rwork0.1968 23567 -
obs0.2002 24877 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.11 Å2 / Biso mean: 58.7062 Å2 / Biso min: 17.82 Å2
Refinement stepCycle: final / Resolution: 2.85→47.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5499 0 0 0 5499
Num. residues----716
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B998X-RAY DIFFRACTION15.175TORSIONAL
12D998X-RAY DIFFRACTION15.175TORSIONAL
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 (%)
2.8501-2.96420.42211420.32782560270299
2.9642-3.0990.33691490.26682536268599
3.099-3.26240.30291390.23552592273199
3.2624-3.46670.311490.24072558270799
3.4667-3.73430.25331450.19752600274599
3.7343-4.10990.24281640.17872587275199
4.1099-4.70410.22041400.14772611275198
4.7041-5.92490.21311460.15812665281198
5.9249-47.19590.25711360.19862858299497
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)
10.30270.15320.09130.85130.05480.73190.0461-0.0202-0.0122-0.0059-0.07540.1098-0.0102-0.0566-00.1916-0.07630.0080.2614-0.08920.327726.9972-27.8772-25.0894
20.31590.0111-0.01161.18750.05140.6463-0.036-0.03590.01660.0219-0.1286-0.0971-0.1334-0.0118-0.0020.2887-0.05040.00890.2337-0.07690.21430.9815-6.2412-23.7392
31.4851-0.18040.83472.16690.03050.9781-0.05410.37790.40710.8062-0.2184-0.1698-0.30910.533-0.32080.6198-0.23220.1395-0.0613-0.36810.044528.417-21.6159-2.1994
40.3142-0.47560.15440.7784-0.17030.4972-0.0028-0.0070.0525-0.0446-0.0266-0.03710.04520.1393-0.00010.19830.0889-0.02210.2778-0.00370.264664.7773-27.43823.7432
50.1661-0.48440.15030.66940.11560.47560.0093-0.04460.1315-0.06880.0217-0.0633-0.1533-0.03140.01810.27070.054-0.02230.20050.03310.26560.876-5.726421.472
61.0284-0.13630.57910.6088-0.15460.7684-0.03860.02350.1628-0.21140.16070.12290.3635-0.04330.0010.40220.02-0.03890.29690.03520.2359.4667-23.1865-0.1832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 96 )A1 - 96
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 239 )A108 - 239
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 152 )B6 - 152
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 96 )C1 - 96
5X-RAY DIFFRACTION5chain 'C' and (resid 108 through 239 )C108 - 239
6X-RAY DIFFRACTION6chain 'D' and (resid 8 through 152)D8 - 152

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