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- PDB-6fjy: Crystal structure of CsuC-CsuE chaperone-tip adhesion subunit pre... -

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Basic information

Entry
Database: PDB / ID: 6fjy
TitleCrystal structure of CsuC-CsuE chaperone-tip adhesion subunit pre-assembly complex from archaic chaperone-usher Csu pili of Acinetobacter baumannii
Components
  • (Protein CsuE) x 2
  • CsuCCalifornia State University, Chico
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 / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
SCPU domain-containing protein / CsuC
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 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
Citation
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Methylation, crystallization and SAD phasing of the Csu pilus CsuC-CsuE chaperone-adhesin subunit pre-assembly complex from Acinetobacter baumannii.
Authors: Pakharukova, N. / Tuittila, M. / Paavilainen, S. / Zavialov, A.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation_author / diffrn_radiation_wavelength
Item: _citation_author.identifier_ORCID / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CsuC
B: Protein CsuE
C: CsuC
D: Protein CsuE


Theoretical massNumber of molelcules
Total (without water)122,9444
Polymers122,9444
Non-polymers00
Water1,71195
1
A: CsuC
B: Protein CsuE


Theoretical massNumber of molelcules
Total (without water)61,4992
Polymers61,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-20 kcal/mol
Surface area23790 Å2
MethodPISA
2
C: CsuC
D: Protein CsuE


Theoretical massNumber of molelcules
Total (without water)61,4452
Polymers61,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-25 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.836, 63.854, 89.245
Angle α, β, γ (deg.)74.650, 79.650, 69.070
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 16 or (resid 17...
21(chain C and (resid 1 through 83 or resid 85...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 16 or (resid 17...A1 - 16
121(chain A and (resid 1 through 16 or (resid 17...A17 - 18
131(chain A and (resid 1 through 16 or (resid 17...A1 - 240
141(chain A and (resid 1 through 16 or (resid 17...A1 - 240
151(chain A and (resid 1 through 16 or (resid 17...A1 - 240
161(chain A and (resid 1 through 16 or (resid 17...A1 - 240
211(chain C and (resid 1 through 83 or resid 85...C1 - 83
221(chain C and (resid 1 through 83 or resid 85...C85 - 93
231(chain C and (resid 1 through 83 or resid 85...C108 - 132
241(chain C and (resid 1 through 83 or resid 85...C133 - 134
251(chain C and (resid 1 through 83 or resid 85...C1 - 239
261(chain C and (resid 1 through 83 or resid 85...C1 - 239
271(chain C and (resid 1 through 83 or resid 85...C1 - 239
281(chain C and (resid 1 through 83 or resid 85...C1 - 239

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Components

#1: Protein CsuC / California State University, Chico


Mass: 27890.615 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) / Strain (production host): AI / References: UniProt: Q6XBY4
#2: Protein Protein CsuE


Mass: 33608.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: APD31_16895, CHQ89_02960 / Plasmid: pET101 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): AI / References: UniProt: A0A0Q1P5T2
#3: Protein Protein CsuE


Mass: 33554.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: APD31_16895, CHQ89_02960 / Plasmid: PET101 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q1P5T2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M bis-Tris, 17% PEG 3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.98
SYNCHROTRONESRF ID23-120.98
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELOct 3, 2015
DECTRIS PILATUS 6M-F2PIXELNov 18, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.981
ReflectionResolution: 2.31→53.925 Å / Num. all: 44881 / Num. obs: 44881 / % possible obs: 96 % / Redundancy: 3.7 % / Biso Wilson estimate: 55.03 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Rsym value: 0.055 / Net I/av σ(I): 9.9 / Net I/σ(I): 13 / Num. measured all: 166711
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
2.31-2.433.50.79212291164620.4890.9350.7921.594.3
2.43-2.583.80.5241.52377162190.3090.610.5242.496.4
2.58-2.763.80.2942.62219758150.1730.3420.2944.196.2
2.76-2.983.80.1674.62058154760.0990.1940.1676.896.5
2.98-3.273.60.098.31772249240.0550.1060.0911.495.3
3.27-3.653.80.05612.81764445880.0330.0650.0561997.5
3.65-4.223.70.0416.61510140330.0240.0470.042696.6
4.22-5.173.60.03220.41191033360.020.0380.03232.795.8
5.17-7.33.70.03419980426280.020.0390.03432.997.1
7.3-53.9253.60.02919.1507014000.0170.0340.02939.594.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→53.925 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 2000 4.46 %
Rwork0.2161 42869 -
obs0.2185 44869 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.58 Å2 / Biso mean: 76.5259 Å2 / Biso min: 29.07 Å2
Refinement stepCycle: final / Resolution: 2.31→53.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7629 0 0 95 7724
Biso mean---49.75 -
Num. residues----995
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1676X-RAY DIFFRACTION16.272TORSIONAL
12C1676X-RAY DIFFRACTION16.272TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.36780.3641410.32623036317795
2.3678-2.43180.34371400.31682975311593
2.4318-2.50330.32711410.293042318396
2.5033-2.58410.33931460.28333109325596
2.5841-2.67650.36051420.26713068321096
2.6765-2.78370.33581440.25533080322496
2.7837-2.91030.31391430.25443059320297
2.9103-3.06380.3371430.25153065320896
3.0638-3.25570.31081410.22813025316695
3.2557-3.5070.28451450.21673113325897
3.507-3.85990.27551450.19773111325697
3.8599-4.41820.22821420.17383041318396
4.4182-5.56550.21081440.16853083322796
5.5655-53.940.25541430.22933062320596
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)
11.93280.28321.03471.69960.67122.58570.01450.0067-0.07-0.09230.08290.0393-0.0637-0.1068-0.08230.28940.0099-0.0060.4095-0.00960.40280.687720.603313.9728
22.51540.79611.2078.73191.22370.6339-0.41160.7295-0.0882-0.4550.178-0.93260.06530.73630.11510.527-0.15580.20420.8104-0.01451.057918.351835.246516.739
33.5483-0.1780.94165.27830.28464.35810.1945-0.74980.01871.0908-0.035-0.41590.2826-0.2165-0.08570.6782-0.0578-0.01910.7281-0.05950.57477.400130.813736.6551
41.37390.0466-1.31071.4629-0.84614.12890.2198-0.1004-0.0386-0.2865-0.10130.07530.06570.3415-0.12230.3610.01780.01330.4205-0.03490.526731.564917.1756-0.9261
54.61481.1735-1.24185.3253-0.76713.75390.1276-0.4092-0.41110.38560.11890.28610.1528-0.1602-0.19980.4347-0.0741-0.0290.51970.06010.4895-6.98914.657930.0368
62.2538-1.145-1.11473.24590.462.66310.07080.3451-0.172-0.7828-0.1050.3223-0.0463-0.13250.01970.63750.0616-0.06140.4799-0.08640.49361.65630.9039-12.191
72.1181-0.3215-0.69816.06852.575.6390.2102-0.1561-0.73550.0285-0.2158-0.05950.98720.957-0.05680.90750.0246-0.16230.61090.11220.87115.1985-21.9118-7.9148
82.97510.0750.01892.4779-0.00662.5180.21180.6343-0.1237-0.9518-0.0437-0.50470.55550.1227-0.08531.24730.08030.06080.6928-0.11770.70239.9143-15.319-27.6226
91.8443-0.1171-1.81211.8459-0.72514.259-0.3649-0.4073-0.465-0.1066-0.3085-0.34310.18370.69620.63840.5539-0.0148-0.15240.52550.15780.867414.0997-12.63316.6087
103.7054-0.58890.19283.6702-1.18152.9970.30390.44740.39980.2675-0.3260.06240.19670.16560.0330.89970.05190.0560.51450.02110.445214.35215.2138-23.4667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 126 )A1 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 143 )A127 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 239 )A144 - 239
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 180 )B1 - 180
5X-RAY DIFFRACTION5chain 'B' and (resid 181 through 312 )B181 - 312
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 126 )C1 - 126
7X-RAY DIFFRACTION7chain 'C' and (resid 127 through 143 )C127 - 143
8X-RAY DIFFRACTION8chain 'C' and (resid 144 through 239 )C144 - 239
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 180 )D1 - 180
10X-RAY DIFFRACTION10chain 'D' and (resid 181 through 239 )D181 - 239

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