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- PDB-9jrq: Pilin PilA from Burkholderia thailandensis -

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Basic information

Entry
Database: PDB / ID: 9jrq
TitlePilin PilA from Burkholderia thailandensis
ComponentsPilin (Bacterial filament) subfamily
KeywordsCELL ADHESION / Pilin / Burkholderia thailandensis / adhesion protein
Function / homologyFimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / cell adhesion / Pilin (Bacterial filament) subfamily
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å
AuthorsLotangchanintra, T. / Wangkanont, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Thailand Science Research and Innovation Fund Chulalongkorn University Thailand
CitationJournal: To Be Published
Title: Pilin PilA from Burkholderia thailandensis
Authors: Lotangchanintra, T. / Wangkanont, K.
History
DepositionSep 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pilin (Bacterial filament) subfamily
B: Pilin (Bacterial filament) subfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,09310
Polymers29,3292
Non-polymers7658
Water7,440413
1
A: Pilin (Bacterial filament) subfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8563
Polymers14,6641
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area7270 Å2
MethodPISA
2
B: Pilin (Bacterial filament) subfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2377
Polymers14,6641
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-9 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.160, 52.810, 73.030
Angle α, β, γ (deg.)90.000, 97.810, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Pilin (Bacterial filament) subfamily


Mass: 14664.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: BTH_I0649 / Plasmid: pET-32b / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T0U4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.09 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 17, 2022
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.25→29.85 Å / Num. obs: 66592 / % possible obs: 99.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.022 / Rrim(I) all: 0.061 / Χ2: 0.93 / Net I/σ(I): 15.5
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3198 / CC1/2: 0.825 / Rpim(I) all: 0.283 / Rrim(I) all: 0.68 / Χ2: 0.91 / % possible all: 94.3

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Processing

Software
NameVersionClassification
MOSFLM7.4.0data reduction
Aimless0.7.9data scaling
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.25→29.85 Å / SU ML: 0.1087 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1873 3272 4.92 %
Rwork0.1541 63290 -
obs0.1558 66562 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.91 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 41 413 2506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582197
X-RAY DIFFRACTIONf_angle_d0.86693025
X-RAY DIFFRACTIONf_chiral_restr0.0793347
X-RAY DIFFRACTIONf_plane_restr0.0072409
X-RAY DIFFRACTIONf_dihedral_angle_d20.4025776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.24831240.22742558X-RAY DIFFRACTION93.35
1.27-1.290.25031140.20982798X-RAY DIFFRACTION98.11
1.29-1.310.24891460.19222682X-RAY DIFFRACTION98.92
1.31-1.330.2391340.17862722X-RAY DIFFRACTION98.65
1.33-1.360.21661520.17242719X-RAY DIFFRACTION98.97
1.36-1.380.19261350.16682739X-RAY DIFFRACTION99.04
1.38-1.410.21551490.16992735X-RAY DIFFRACTION99.24
1.41-1.440.22491450.15642728X-RAY DIFFRACTION99.31
1.44-1.470.17121380.14062780X-RAY DIFFRACTION99.39
1.47-1.510.1821470.13472741X-RAY DIFFRACTION99.55
1.51-1.550.17091500.13372727X-RAY DIFFRACTION99.52
1.55-1.60.16821380.13762776X-RAY DIFFRACTION99.69
1.6-1.650.17991300.14032735X-RAY DIFFRACTION99.79
1.65-1.710.17841380.14312802X-RAY DIFFRACTION99.83
1.71-1.780.16981520.14452756X-RAY DIFFRACTION99.93
1.78-1.860.17121480.15012735X-RAY DIFFRACTION99.97
1.86-1.960.18241310.15082783X-RAY DIFFRACTION100
1.96-2.080.15891560.14732764X-RAY DIFFRACTION100
2.08-2.240.18981380.15442785X-RAY DIFFRACTION100
2.24-2.460.1961310.15562820X-RAY DIFFRACTION100
2.46-2.820.19631590.16172779X-RAY DIFFRACTION100
2.82-3.550.18071420.15982801X-RAY DIFFRACTION100
3.55-29.850.18761750.14742825X-RAY DIFFRACTION99.8

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