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- PDB-2rjz: Crystal structure of the type 4 fimbrial biogenesis protein PilO ... -

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Basic information

Entry
Database: PDB / ID: 2rjz
TitleCrystal structure of the type 4 fimbrial biogenesis protein PilO from Pseudomonas aeruginosa
ComponentsPilO protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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 / Helix hairpin bin / Ribosomal protein S6/Translation elongation factor EF1B / Translation elongation factor EF1B/ribosomal protein S6 / Helix Hairpins / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Chang, S. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric complex.
Authors: Sampaleanu, L.M. / Bonanno, J.B. / Ayers, M. / Koo, J. / Tammam, S. / Burley, S.K. / Almo, S.C. / Burrows, L.L. / Howell, P.L.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: PilO protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2726
Polymers32,8872
Non-polymers3844
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.471, 70.471, 116.876
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-316-

HOH

DetailsAuthors state that the biological unit assembly shown in remark 350 is probable.

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Components

#1: Protein PilO protein / Type 4 fimbrial biogenesis protein PilO


Mass: 16443.709 Da / Num. of mol.: 2 / Fragment: Residues 69-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: pilO / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q51353
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8
Details: 100 mM Tris-HCl pH 8.0, 2 M Ammonium sulfate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.2→61.085 Å / Num. all: 16706 / Num. obs: 16706 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3 / Num. unique all: 2406 / Rsym value: 0.557 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
DENZOdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.733 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.245 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SEMET MODELED AS MET
RfactorNum. reflection% reflectionSelection details
Rfree0.234 841 5.1 %RANDOM
Rwork0.193 ---
obs0.195 16636 99.97 %-
all-16636 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.058 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 20 95 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222160
X-RAY DIFFRACTIONr_angle_refined_deg1.4582.0012924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08824.61591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69515389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8951510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021584
X-RAY DIFFRACTIONr_nbd_refined0.2120.2902
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.24
X-RAY DIFFRACTIONr_mcbond_it1.0781.51385
X-RAY DIFFRACTIONr_mcangle_it1.55222149
X-RAY DIFFRACTIONr_scbond_it2.4683883
X-RAY DIFFRACTIONr_scangle_it3.7974.5773
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 54 -
Rwork0.251 1147 -
all-1201 -
obs-1147 99.92 %

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