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- PDB-9jw7: Pilin PilA from Burkholderia pseudomallei -

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Basic information

Entry
Database: PDB / ID: 9jw7
TitlePilin PilA from Burkholderia pseudomallei
ComponentsPilA
KeywordsCELL ADHESION / Pilin / Burkholderia pseudomallei / adhesion protein
Function / homologyFimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / cell adhesion / membrane / PilA
Function and homology information
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
Authors: Lotangchanintra, L. / 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

Downloads & links

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Assembly

Deposited unit
A: PilA


Theoretical massNumber of molelcules
Total (without water)14,5481
Polymers14,5481
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.560, 50.560, 49.990
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
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: 1.45→29.08 Å / Num. obs: 22367 / % possible obs: 99.7 % / Redundancy: 15 % / Biso Wilson estimate: 21.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.018 / Rrim(I) all: 0.069 / Χ2: 0.94 / Net I/σ(I): 19.6
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.141 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1084 / CC1/2: 0.772 / Rpim(I) all: 0.303 / Rrim(I) all: 1.181 / Χ2: 0.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOSFLM7.4.0data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→29.08 Å / SU ML: 0.1756 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 1181 5.28 %
Rwork0.2097 21168 -
obs0.2108 22349 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.39 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 0 158 1181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691073
X-RAY DIFFRACTIONf_angle_d0.94641477
X-RAY DIFFRACTIONf_chiral_restr0.0729173
X-RAY DIFFRACTIONf_plane_restr0.0079203
X-RAY DIFFRACTIONf_dihedral_angle_d13.0361379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.520.34271360.29982611X-RAY DIFFRACTION99.1
1.52-1.60.27831390.25752630X-RAY DIFFRACTION99.64
1.6-1.70.30731450.26742649X-RAY DIFFRACTION99.61
1.7-1.830.25971760.2412595X-RAY DIFFRACTION99.78
1.83-2.010.29481380.25372652X-RAY DIFFRACTION99.93
2.01-2.30.24691490.23332669X-RAY DIFFRACTION99.96
2.3-2.90.26431350.21752668X-RAY DIFFRACTION100
2.9-29.080.17941630.17032694X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 15.1784431757 Å / Origin y: 2.17802362625 Å / Origin z: 5.27526939599 Å
111213212223313233
T0.136249687036 Å20.00493592819269 Å2-0.0164095135589 Å2-0.0964777148069 Å20.0148636698709 Å2--0.127172719075 Å2
L3.28676113665 °21.38439453531 °22.72010491915 °2-2.67571426454 °23.46704283409 °2--6.23485785578 °2
S0.271491958688 Å °-0.0486061621899 Å °-0.349201014286 Å °0.139905868309 Å °0.117774167243 Å °-0.346764134839 Å °0.267393724334 Å °-0.0518799751341 Å °-0.154939097148 Å °
Refinement TLS groupSelection details: chain A

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