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- PDB-9jw8: Pilin PilA from Burkholderia pseudomallei with iodide ions -

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Basic information

Entry
Database: PDB / ID: 9jw8
TitlePilin PilA from Burkholderia pseudomallei with iodide ions
ComponentsPilA
KeywordsCELL ADHESION / Pilin / Burkholderia pseudomallei / adhesion protein
Function / homology
Function and homology information


pilus / cell adhesion / membrane
Similarity search - Function
Fimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsLotangchanintra, T. / Wangkanont, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Other governmentThailand Science Research and Innovation Fund Chulalongkorn University Thailand
CitationJournal: To Be Published
Title: Pilin PilA from Burkholderia pseudomallei with iodide ions
Authors: Lotangchanintra, T. / Wangkanont, K.
History
DepositionOct 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PilA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8023
Polymers14,5481
Non-polymers2542
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-0 kcal/mol
Surface area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.420, 50.420, 50.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein PilA


Mass: 14548.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Gene: pilA, Y036_1241 / Plasmid: pET-32b / Production host: Escherichia coli (E. coli) / References: UniProt: Q6J5K8
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 25% PEG 4,000

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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: 1.5→29.09 Å / Num. obs: 20076 / % possible obs: 99 % / Redundancy: 14.9 % / Biso Wilson estimate: 19.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.019 / Rrim(I) all: 0.074 / Χ2: 1.01 / Net I/σ(I): 20.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 3 / Num. unique obs: 901 / CC1/2: 0.748 / Rpim(I) all: 0.249 / Rrim(I) all: 0.877 / Χ2: 0.9 / % possible all: 91.1

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Processing

Software
NameVersionClassification
MOSFLM7.4.0data reduction
Aimless0.7.9data scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→29.09 Å / SU ML: 0.147 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 1012 5.04 %
Rwork0.1894 19049 -
obs0.191 20061 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.97 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 2 188 1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671057
X-RAY DIFFRACTIONf_angle_d0.96421452
X-RAY DIFFRACTIONf_chiral_restr0.0577170
X-RAY DIFFRACTIONf_plane_restr0.0093199
X-RAY DIFFRACTIONf_dihedral_angle_d12.9635372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.29191320.25152618X-RAY DIFFRACTION95.39
1.58-1.680.25611610.21992675X-RAY DIFFRACTION98.75
1.68-1.810.24211410.21122718X-RAY DIFFRACTION99.17
1.81-1.990.18581320.21182749X-RAY DIFFRACTION99.55
1.99-2.280.21781100.20812769X-RAY DIFFRACTION99.58
2.28-2.870.24682010.20422698X-RAY DIFFRACTION99.86
2.87-29.090.19691350.16032822X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 15.2743527337 Å / Origin y: 2.07166715737 Å / Origin z: 5.27461738587 Å
111213212223313233
T0.0931530236888 Å20.00841165163266 Å20.00423520271559 Å2-0.0728191392391 Å20.00909531400079 Å2--0.144172806742 Å2
L1.79853547372 °20.826637888548 °21.64351944028 °2-1.32258572959 °22.2885543173 °2--5.32810215648 °2
S0.212318239401 Å °0.00519164640558 Å °-0.203877233505 Å °0.0119087071264 Å °0.0549595472448 Å °-0.194731670823 Å °0.111076815134 Å °-0.0351663118882 Å °-0.123896603111 Å °
Refinement TLS groupSelection details: chain A

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