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- PDB-9jr8: Pilin PilA from Burkholderia thailandensis with iodide ions -

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Basic information

Entry
Database: PDB / ID: 9jr8
TitlePilin PilA from Burkholderia thailandensis with iodide ions
ComponentsPilin (Bacterial filament) subfamily
KeywordsCELL ADHESION / Pilin / Burkholderia thailandensis
Function / homologyFimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / cell adhesion / IODIDE ION / Pilin (Bacterial filament) subfamily
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 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 with iodide ions
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

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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)32,63229
Polymers29,3292
Non-polymers3,30327
Water5,008278
1
A: Pilin (Bacterial filament) subfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,50616
Polymers14,6641
Non-polymers1,84215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pilin (Bacterial filament) subfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,12513
Polymers14,6641
Non-polymers1,46112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.230, 52.605, 73.325
Angle α, β, γ (deg.)90.000, 97.440, 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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
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: 1.55→29.91 Å / Num. obs: 34806 / % possible obs: 98.4 % / Redundancy: 15.3 % / Biso Wilson estimate: 16.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.028 / Rrim(I) all: 0.109 / Χ2: 0.95 / Net I/σ(I): 18.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.466 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1661 / CC1/2: 0.825 / Rpim(I) all: 0.396 / Rrim(I) all: 1.519 / Χ2: 0.78 / % possible all: 97.5

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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: 1.55→29.91 Å / SU ML: 0.1837 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 1754 5.04 %
Rwork0.1859 33034 -
obs0.1875 34788 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.99 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 43 278 2373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622143
X-RAY DIFFRACTIONf_angle_d0.92172943
X-RAY DIFFRACTIONf_chiral_restr0.0578343
X-RAY DIFFRACTIONf_plane_restr0.0079397
X-RAY DIFFRACTIONf_dihedral_angle_d13.8551757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.29111140.24982505X-RAY DIFFRACTION97.22
1.59-1.640.27671410.23252469X-RAY DIFFRACTION96.85
1.64-1.690.28291310.222520X-RAY DIFFRACTION97.21
1.69-1.750.24821410.21832505X-RAY DIFFRACTION97.6
1.75-1.820.26921170.20922521X-RAY DIFFRACTION97.67
1.82-1.910.2181450.19192526X-RAY DIFFRACTION97.8
1.91-2.010.21191490.18942517X-RAY DIFFRACTION98.27
2.01-2.130.24861140.19012548X-RAY DIFFRACTION98.37
2.13-2.30.23811620.19272536X-RAY DIFFRACTION98.58
2.3-2.530.19711260.18832564X-RAY DIFFRACTION99.04
2.53-2.890.23111340.18752581X-RAY DIFFRACTION99.09
2.89-3.640.20641470.17312589X-RAY DIFFRACTION99.49
3.64-29.910.17641330.1632653X-RAY DIFFRACTION99.68

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