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- PDB-1oqw: Full-Length PAK Pilin from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1oqw
TitleFull-Length PAK Pilin from Pseudomonas aeruginosa
ComponentsFimbrial protein
KeywordsCELL ADHESION / Type IV pilin / fiber-forming protein / adhesion / Pseudomonas aerugionosa / PAK pilin
Function / homology
Function and homology information


type IV pilus / type IV pilus-dependent motility / cell adhesion / membrane
Similarity search - Function
Glycoprotein, Type 4 Pilin / Glycoprotein, Type 4 Pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCraig, L. / Arvai, A.S. / Forest, K.T. / Tainer, J.A.
CitationJournal: Mol.Cell / Year: 2003
Title: Type IV Pilin Structure and Assembly: X-Ray and EM Analyses of Vibrio cholerae Toxin-Coregulated Pilus and Pseudomonas aeruginosa PAK Pilin
Authors: Craig, L. / Taylor, R.K. / Pique, M.E. / Adair, B.A. / Arvai, A.S. / Singh, M. / Lloyd, S.J. / Shin, D.S. / Getzoff, E.D. / Yeager, M. / Forest, K.T. / Tainer, J.A.
History
DepositionMar 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fimbrial protein
B: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)30,0422
Polymers30,0422
Non-polymers00
Water5,080282
1
A: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)15,0211
Polymers15,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)15,0211
Polymers15,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.015, 44.422, 73.782
Angle α, β, γ (deg.)90.00, 116.82, 90.00
Int Tables number5
Space group name H-MC121
Detailsthousands of pilin subunits assemble to form a long thin filament ~8 nm in diameter and several microns in length

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Components

#1: Protein Fimbrial protein / Pilin / Strain PAK


Mass: 15021.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: K / References: UniProt: P02973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 3.21 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% MPD, 35% PEG 4000, 100 mM sodium citrate, 2.5 mM MnCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
215 %MPD1reservoir
335 %PEG40001reservoir
4100 mMsodium citrate1reservoirpH5.6
52.5 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 29079 / Num. obs: 28468 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.24 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.28 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2875 / % possible all: 83.6
Reflection
*PLUS
Num. obs: 29308 / Num. measured all: 324152
Reflection shell
*PLUS
% possible obs: 83.6 % / Rmerge(I) obs: 0.329

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZO.pdb

1dzo


Resolution: 2→30 Å / Cross valid method: used throughout refinement / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1322 -random
Rwork0.223 ---
all0.219 29079 --
obs0.225 27307 93.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.86 Å20 Å21.12 Å2
2---1.062 Å20 Å2
3----3.798 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 0 282 2392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2→2.3 Å /
RfactorNum. reflection
Rfree0.28 42
Rwork0.28 -
obs-772
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.007

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