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- PDB-5uvr: The core region of PilO from the type IV pilus system of Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 5uvr
TitleThe core region of PilO from the type IV pilus system of Pseudomonas aeruginosa
ComponentsPilO protein
KeywordsMEMBRANE PROTEIN / alignment subcomplex / modified ferredoxin fold / reductive methylation / type iv pili
Function / homology
Function and homology information


oligosaccharyl transferase activity / type IV pilus assembly / type IV pilus-dependent motility / membrane
Similarity search - Function
Type IV pilus inner membrane component PilO / Pilus assembly protein, PilO / Ribosomal protein S6/Translation elongation factor EF1B / Translation elongation factor EF1B/ribosomal protein S6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHowell, P.L. / Junop, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-93585 Canada
CitationJournal: Sci Rep / Year: 2018
Title: Conserved, unstructured regions in Pseudomonas aeruginosa PilO are important for type IVa pilus function.
Authors: Leighton, T.L. / Mok, M.C. / Junop, M.S. / Howell, P.L. / Burrows, L.L.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: PilO protein


Theoretical massNumber of molelcules
Total (without water)10,8141
Polymers10,8141
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PilO protein

A: PilO protein


Theoretical massNumber of molelcules
Total (without water)21,6272
Polymers21,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area1170 Å2
ΔGint-12 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.810, 40.810, 250.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

21A-379-

HOH

31A-397-

HOH

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Components

#1: Protein PilO protein / Pilus assembly protein / PilO


Mass: 10813.502 Da / Num. of mol.: 1 / Fragment: core region (UNP residues 109-206)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pilO, PAERUG_E15_London_28_01_14_03389, PAERUG_P32_London_17_VIM_2_10_11_01500
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q51353
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaCl, 0.1 M CAPS pH 10.5, 20% (v/v) PEG 8000), 3% (v/v) DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→35.342 Å / Num. obs: 14759 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata processing
PHENIXphasing
PHENIXmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RJZ

2rjz


Resolution: 1.7→35.342 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.64
RfactorNum. reflection% reflection
Rfree0.2674 1468 9.99 %
Rwork0.2311 --
obs0.2347 14688 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→35.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 0 97 849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006767
X-RAY DIFFRACTIONf_angle_d0.8261042
X-RAY DIFFRACTIONf_dihedral_angle_d8.826458
X-RAY DIFFRACTIONf_chiral_restr0.055123
X-RAY DIFFRACTIONf_plane_restr0.006132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.76080.31921400.28911259X-RAY DIFFRACTION100
1.7608-1.83130.29021400.26821264X-RAY DIFFRACTION100
1.8313-1.91470.311420.25691277X-RAY DIFFRACTION100
1.9147-2.01560.30761450.25121295X-RAY DIFFRACTION100
2.0156-2.14190.30891430.24671307X-RAY DIFFRACTION100
2.1419-2.30720.25171450.23861295X-RAY DIFFRACTION100
2.3072-2.53930.29561460.25021327X-RAY DIFFRACTION100
2.5393-2.90660.28721500.24311339X-RAY DIFFRACTION100
2.9066-3.66150.23961500.21311362X-RAY DIFFRACTION100
3.6615-35.35010.24831670.21491495X-RAY DIFFRACTION99

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