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- PDB-6fm5: Crystal structure of self-complemented CsuA/B major subunit from ... -

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Basic information

Entry
Database: PDB / ID: 6fm5
TitleCrystal structure of self-complemented CsuA/B major subunit from archaic chaperone-usher Csu pili of Acinetobacter baumannii
ComponentsCsuA/B,CsuA/B,CsuA/B,CsuA/B
KeywordsCELL ADHESION / Ig-like fold / beta sandwich / donor-strand complementation
Function / homologySpore coat protein U / Spore Coat Protein U domain / Spore Coat Protein U domain / CsuA/B
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 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
DepositionJan 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CsuA/B,CsuA/B,CsuA/B,CsuA/B


Theoretical massNumber of molelcules
Total (without water)17,6431
Polymers17,6431
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.214, 92.018, 34.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

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Components

#1: Protein CsuA/B,CsuA/B,CsuA/B,CsuA/B


Mass: 17643.277 Da / Num. of mol.: 1
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 28-30% PEG, 0.2 M ammonium sulfate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.8726
SYNCHROTRONESRF ID23-120.979
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELJun 16, 2015
DECTRIS PILATUS 6M-F2PIXELMay 16, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
20.9791
ReflectionResolution: 1.47→49.21 Å / Num. obs: 27069 / % possible obs: 99.7 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.033 / Rrim(I) all: 0.07 / Net I/σ(I): 12.1 / Num. measured all: 116430
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.524.10.7411060825910.6330.4120.8521.899.5
5.69-49.2140.03121875460.9980.0170.03633.999.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALA0.5.9data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→46.009 Å / FOM work R set: 0.8506 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 1355 5.01 %
Rwork0.1967 25664 -
obs0.1979 27019 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.55 Å2 / Biso mean: 19.69 Å2 / Biso min: 7.5 Å2
Refinement stepCycle: final / Resolution: 1.47→46.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 0 171 1308
Biso mean---27.13 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111153
X-RAY DIFFRACTIONf_angle_d1.371573
X-RAY DIFFRACTIONf_chiral_restr0.084191
X-RAY DIFFRACTIONf_plane_restr0.005209
X-RAY DIFFRACTIONf_dihedral_angle_d11.639394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.52260.30281270.26962508263599
1.5226-1.58350.32031370.25325392676100
1.5835-1.65560.23951100.230625532663100
1.6556-1.74290.24371550.215325142669100
1.7429-1.85210.22391250.19725582683100
1.8521-1.99510.20391470.178625502697100
1.9951-2.19590.21151370.17352530266799
2.1959-2.51360.18881360.181425692705100
2.5136-3.16680.21681490.201726212770100
3.1668-46.03150.21511320.19332722285499

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