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- PDB-6fq0: Crystal structure of the CsuC-CsuA/B chaperone-subunit preassembl... -

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Basic information

Entry
Database: PDB / ID: 6fq0
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 / Immunoglobulins ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsPakharukova, N.A. / 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 12, 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 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
Water3,261181
1
A: CsuC
B: CsuA/B,CsuA/B


Theoretical massNumber of molelcules
Total (without water)42,9352
Polymers42,9352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-16 kcal/mol
Surface area16270 Å2
MethodPISA
2
C: CsuC
D: CsuA/B,CsuA/B


Theoretical massNumber of molelcules
Total (without water)42,9352
Polymers42,9352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-15 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.419, 111.419, 167.745
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 207 or resid 216 through 239))
21(chain C and (resid 1 through 96 or resid 108 through 182 or resid 195 through 239))
12(chain B and (resid 9 through 83 or resid 85 or resid 89 through 152))
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAILEILE(chain A and (resid 1 through 207 or resid 216 through 239))AA1 - 2071 - 207
121ALAALAMETMET(chain A and (resid 1 through 207 or resid 216 through 239))AA216 - 239216 - 239
211ALAALAPROPRO(chain C and (resid 1 through 96 or resid 108 through 182 or resid 195 through 239))CC1 - 961 - 96
221SERSERLYSLYS(chain C and (resid 1 through 96 or resid 108 through 182 or resid 195 through 239))CC108 - 182108 - 182
231GLYGLYMETMET(chain C and (resid 1 through 96 or resid 108 through 182 or resid 195 through 239))CC195 - 239195 - 239
112HISHISLYSLYS(chain B and (resid 9 through 83 or resid 85 or resid 89 through 152))BB9 - 839 - 83
122THRTHRTHRTHR(chain B and (resid 9 through 83 or resid 85 or resid 89 through 152))BB8585
132ASPASPPHEPHE(chain B and (resid 9 through 83 or resid 85 or resid 89 through 152))BB89 - 15289 - 152
212HISHISPHEPHEchain DDD9 - 1529 - 152

NCS ensembles :
ID
1
2

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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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium malate, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→83.641 Å / Num. all: 24003 / Num. obs: 24003 / % possible obs: 89.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 41.48 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Rsym value: 0.041 / Net I/av σ(I): 14.9 / Net I/σ(I): 20.2 / Num. measured all: 79742
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
2.5-2.643.10.24531100935550.1580.2930.245590.2
2.64-2.83.40.1584.71164534300.0980.1860.1587.892.3
2.8-2.993.40.1076.81094031950.0660.1270.10711.291.7
2.99-3.233.40.06710.61000429340.0420.080.06716.490.7
3.23-3.543.40.0514.2910626700.0310.0590.0522.589.2
3.54-3.953.30.03519.6792623830.0220.0420.0353088
3.95-4.563.10.02723.4644120470.0170.0330.0273686.4
4.56-5.593.20.02427.1549517380.0150.0290.02438.885.3
5.59-7.913.50.02724.5470313350.0160.0310.02736.786.7
7.91-55.713.50.02127.624737160.0130.0250.02148.384.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→55.709 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 1236 5.15 %
Rwork0.1894 22766 -
obs0.192 24002 89.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.85 Å2 / Biso mean: 49.7438 Å2 / Biso min: 17.56 Å2
Refinement stepCycle: final / Resolution: 2.5→55.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5133 0 0 181 5314
Biso mean---46.23 -
Num. residues----668
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1930X-RAY DIFFRACTION5.757TORSIONAL
12C1930X-RAY DIFFRACTION5.757TORSIONAL
21B1073X-RAY DIFFRACTION5.757TORSIONAL
22D1073X-RAY DIFFRACTION5.757TORSIONAL
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 (%)
2.5001-2.60020.31431280.2462558268689
2.6002-2.71850.26251230.21622638276192
2.7185-2.86180.3071650.21982595276092
2.8618-3.04110.29231390.21822592273191
3.0411-3.27590.30791270.21062575270291
3.2759-3.60550.23481370.19092490262789
3.6055-4.12710.1981400.16512478261888
4.1271-5.19920.171340.1442403253785
5.1992-55.72330.25151430.20412437258086
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)
14.03961.3942-0.43283.0963-1.03593.3164-0.14110.03420.12910.22320.09640.0916-0.357-0.24740.0390.26940.0118-0.0170.23820.01380.1974-38.049119.0038-8.8167
22.68790.531-0.95171.67320.13073.9425-0.23470.1104-0.38890.04760.0894-0.4398-0.04280.66850.12630.3284-0.05070.03540.32910.04380.3704-17.615814.6477-8.8375
31.79890.3114-0.30513.37530.17524.13060.1512-0.13810.15610.5225-0.1972-0.1413-0.6758-0.16420.0050.5188-0.0019-0.04140.20120.00410.3195-33.889315.330515.3997
43.9551-1.24350.59593.0511-1.23323.5856-0.13520.0737-0.3015-0.14460.12220.13120.3995-0.2913-0.00270.2795-0.01180.00970.2321-0.00760.2364-38.0563-18.989830.2959
52.42380.08440.9031.09590.23884.1385-0.2406-0.05720.3083-0.07040.0409-0.2732-0.06760.74440.18890.3580.0553-0.0310.35760.02570.4133-17.9763-14.303930.4489
61.6855-0.54840.26652.7530.11124.36230.23250.1987-0.1412-0.5203-0.2361-0.14940.705-0.23290.00470.56420.02030.04910.23910.00510.2963-33.7562-15.24295.8927
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 8 through 152 )B8 - 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 9 through 152 )D9 - 152

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