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- PDB-9ime: Pilin PilA from Burkholderia thailandensis with bromide ions -

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Basic information

Entry
Database: PDB / ID: 9ime
TitlePilin PilA from Burkholderia thailandensis with bromide ions
ComponentsPilin (Bacterial filament) subfamily
KeywordsCELL ADHESION / Pilin / Burkholderia
Function / homologyFimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / cell adhesion / BROMIDE ION / Pilin (Bacterial filament) subfamily
Function and homology information
Biological speciesBurkholderia thailandensis E264 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsLotangchanintra, T. / Wawrzak, Z. / Wangkanont, K.
Funding support1items
OrganizationGrant numberCountry
Other governmentThailand Science Research and Innovation Fund Chulalongkorn University
CitationJournal: To Be Published
Title: Pilin PilA from Burkholderia thailandensis with bromide ions
Authors: Lotangchanintra, T. / Wawrzak, Z. / Wangkanont, K.
History
DepositionJul 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 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)31,68829
Polymers29,3292
Non-polymers2,36027
Water6,792377
1


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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.245, 52.720, 72.885
Angle α, β, γ (deg.)90.000, 97.600, 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 E264 (bacteria)
Gene: BTH_I0649 / Plasmid: pET-32b / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T0U4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 41.48 %
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-D / Wavelength: 0.91163 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91163 Å / Relative weight: 1
ReflectionResolution: 1.35→29.8 Å / Num. obs: 102670 / % possible obs: 98.3 % / Redundancy: 20.9 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.033 / Rrim(I) all: 0.108 / Χ2: 0.99 / Net I/σ(I): 18
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 19.7 % / Rmerge(I) obs: 1.938 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2528 / CC1/2: 0.763 / Rpim(I) all: 0.635 / Rrim(I) all: 2.041 / Χ2: 0.93 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLM7.4.0data reduction
Aimless0.7.9data scaling
PHENIX1.20.1phasing
PHENIX1.20.1model building
RefinementMethod to determine structure: SAD / Resolution: 1.35→29.8 Å / SU ML: 0.1548 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1882 5045 4.91 %
Rwork0.1548 97612 -
obs0.1564 102657 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.13 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 89 377 2518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612284
X-RAY DIFFRACTIONf_angle_d0.88263144
X-RAY DIFFRACTIONf_chiral_restr0.0781355
X-RAY DIFFRACTIONf_plane_restr0.0076424
X-RAY DIFFRACTIONf_dihedral_angle_d20.3817811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.34371480.28213227X-RAY DIFFRACTION97.94
1.37-1.380.26621920.26433187X-RAY DIFFRACTION97.01
1.38-1.40.28811520.25433205X-RAY DIFFRACTION94.8
1.4-1.420.33891480.24263214X-RAY DIFFRACTION97.7
1.42-1.430.26571810.22463271X-RAY DIFFRACTION98.21
1.43-1.450.26131740.20263149X-RAY DIFFRACTION96.1
1.45-1.470.24131890.193195X-RAY DIFFRACTION96.55
1.48-1.50.21711720.18293218X-RAY DIFFRACTION98.6
1.5-1.520.21331520.17563251X-RAY DIFFRACTION97.4
1.52-1.550.21321900.16743264X-RAY DIFFRACTION96.62
1.55-1.570.24191390.16533206X-RAY DIFFRACTION98.82
1.57-1.60.16831680.15683269X-RAY DIFFRACTION97.5
1.6-1.630.19551460.15633221X-RAY DIFFRACTION97.45
1.63-1.660.1831830.15333273X-RAY DIFFRACTION98.86
1.66-1.70.21581770.15113250X-RAY DIFFRACTION96.84
1.7-1.740.19371790.14793203X-RAY DIFFRACTION99.27
1.74-1.780.20621590.14013267X-RAY DIFFRACTION98
1.78-1.830.18851860.13533225X-RAY DIFFRACTION98.64
1.83-1.890.17081470.13573364X-RAY DIFFRACTION98.57
1.89-1.950.1981730.13213219X-RAY DIFFRACTION98.81
1.95-2.020.15921620.13953292X-RAY DIFFRACTION98.12
2.02-2.10.22211570.13863276X-RAY DIFFRACTION99.68
2.1-2.190.1651820.14043303X-RAY DIFFRACTION98.89
2.19-2.310.16311750.13993273X-RAY DIFFRACTION99.02
2.31-2.450.14141680.13743294X-RAY DIFFRACTION99.74
2.45-2.640.20851960.15843247X-RAY DIFFRACTION99.51
2.64-2.910.17611520.15633370X-RAY DIFFRACTION99.52
2.91-3.330.18361800.15493260X-RAY DIFFRACTION99.71
3.33-4.190.14021560.13293316X-RAY DIFFRACTION99.86
4.19-29.80.1911620.1683303X-RAY DIFFRACTION99.31

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