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- PDB-8q8o: PA14_16140 protein: the regulator of an operon involved in the bi... -

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Basic information

Entry
Database: PDB / ID: 8q8o
TitlePA14_16140 protein: the regulator of an operon involved in the biofilm formation in PA14 P. aeruginosa
ComponentsDUF2170 family protein
KeywordsCHAPERONE / regulator / biofilm / pseudomonas
Function / homologyProtein of unknown function DUF2170 / Uncharacterized protein conserved in bacteria (DUF2170) / Tb-Xo4 / DUF2170 family protein
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsBroutin, I. / Phan, G. / Girard, E.
Funding support France, 1items
OrganizationGrant numberCountry
Not funded France
CitationJournal: Front Microbiol / Year: 2024
Title: BacA: a possible regulator that contributes to the biofilm formation of Pseudomonas aeruginosa .
Authors: Wallart, L. / Ben Mlouka, M.A. / Saffiedine, B. / Coquet, L. / Le, H. / Hardouin, J. / Jouenne, T. / Phan, G. / Kiefer-Meyer, M.C. / Girard, E. / Broutin, I. / Cosette, P.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF2170 family protein
B: DUF2170 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3224
Polymers31,6742
Non-polymers6482
Water48627
1
A: DUF2170 family protein
hetero molecules

A: DUF2170 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8584
Polymers31,6742
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
2
B: DUF2170 family protein
hetero molecules

B: DUF2170 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7864
Polymers31,6742
Non-polymers1,1132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Unit cell
Length a, b, c (Å)68.862, 68.862, 281.073
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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Components

#1: Protein DUF2170 family protein


Mass: 15836.769 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: PA14_16140 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A0H2ZF40
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.93 Å3/Da / Density % sol: 58 % / Description: long needle
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 32% PEG 200, 0.2M NaCl, 0.1M acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.649 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.649 Å / Relative weight: 1
ReflectionResolution: 2.7→46.85 Å / Num. obs: 11686 / % possible obs: 99.7 % / Redundancy: 21.4 % / Biso Wilson estimate: 40.66 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.037 / Rrim(I) all: 0.173 / Net I/σ(I): 22.9
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 5 / Num. unique obs: 1478 / CC1/2: 0.95 / Rpim(I) all: 0.243 / Rrim(I) all: 1.126 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→46.85 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2688 1152 10 %
Rwork0.2103 --
obs0.2162 11472 98.06 %
Displacement parametersBiso mean: 46.96 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 36 27 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112208
X-RAY DIFFRACTIONf_angle_d0.5753027
X-RAY DIFFRACTIONf_chiral_restr0.0387350
X-RAY DIFFRACTIONf_plane_restr0.0025379
X-RAY DIFFRACTIONf_dihedral_angle_d17.9406786

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