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- PDB-8eju: The crystal structure of Pseudomonas putida PcaR -

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Basic information

Entry
Database: PDB / ID: 8eju
TitleThe crystal structure of Pseudomonas putida PcaR
ComponentsTranscription regulatory protein (Pca regulon)
KeywordsTRANSCRIPTION / Apo / Transcription Factor / Gene Regulation
Function / homology
Function and homology information


3,4-dihydroxybenzoate metabolic process / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
Beta-ketoadipate transcriptional regulator, PcaR/PcaU/PobR / helix_turn_helix isocitrate lyase regulation / IclR helix-turn-helix domain / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / : / Bacterial transcriptional regulator IclR C-terminal / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF-like domain superfamily ...Beta-ketoadipate transcriptional regulator, PcaR/PcaU/PobR / helix_turn_helix isocitrate lyase regulation / IclR helix-turn-helix domain / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / : / Bacterial transcriptional regulator IclR C-terminal / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / selenourea / Transcription regulatory protein (Pca regulon)
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsPham, C. / Skarina, T. / Di Leo, R. / Stogios, P.J. / Mahadevan, R. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Ontario Research FundBiochemicals from Cellulosic Biomass (BioCeB) Canada
CitationJournal: Febs J. / Year: 2024
Title: Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors.
Authors: Pham, C. / Nasr, M.A. / Skarina, T. / Di Leo, R. / Kwan, D.H. / Martin, V.J.J. / Stogios, P.J. / Mahadevan, R. / Savchenko, A.
History
DepositionSep 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription regulatory protein (Pca regulon)
B: Transcription regulatory protein (Pca regulon)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,81120
Polymers63,5572
Non-polymers1,25518
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-165 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.903, 148.903, 55.711
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

#1: Protein Transcription regulatory protein (Pca regulon)


Mass: 31778.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
Gene: pcaR, PP_1375 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic / References: UniProt: Q88N41
#2: Chemical
ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH4N2Se
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.8 M ammonium phosphate monobasic, 0.1 M sodium acetate, pH 4.6, 1% ethylene glycol, 2.5% 1-butyl-2,3-dimethylimidazolium tetrafluoroborate, soak with selenourea

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.925 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.925 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 87124 / % possible obs: 99.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 29.73 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.107 / Net I/σ(I): 34.3
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 3679 / CC1/2: 0.825 / Rpim(I) all: 0.263 / Rrim(I) all: 0.664

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IA2

2ia2


Resolution: 1.74→48.74 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 2002 2.78 %RANDOM
Rwork0.1762 69917 --
obs0.1774 71919 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.37 Å2
Refinement stepCycle: LAST / Resolution: 1.74→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3951 0 45 437 4433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01444059
X-RAY DIFFRACTIONf_angle_d1.40175506
X-RAY DIFFRACTIONf_chiral_restr0.0884649
X-RAY DIFFRACTIONf_plane_restr0.0122712
X-RAY DIFFRACTIONf_dihedral_angle_d13.4281500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.28951400.2484791X-RAY DIFFRACTION96.27
1.79-1.830.23321440.21654975X-RAY DIFFRACTION99.81
1.83-1.890.25611430.2244939X-RAY DIFFRACTION99.9
1.89-1.950.35641420.29154956X-RAY DIFFRACTION99.14
1.95-2.020.27211440.20894988X-RAY DIFFRACTION99.86
2.02-2.10.20881420.17724975X-RAY DIFFRACTION99.94
2.1-2.20.19891430.17615007X-RAY DIFFRACTION99.94
2.2-2.310.22871430.18554988X-RAY DIFFRACTION99.84
2.31-2.460.23231390.17995006X-RAY DIFFRACTION100
2.46-2.650.21681460.17555006X-RAY DIFFRACTION99.96
2.65-2.910.2151430.18535018X-RAY DIFFRACTION99.96
2.91-3.330.21731460.1675034X-RAY DIFFRACTION99.98
3.33-4.20.18341410.14525067X-RAY DIFFRACTION99.98
4.2-48.740.22311460.17325167X-RAY DIFFRACTION99.72
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.141513974140.530768767157-0.9416714535882.01147701503-0.05168229357761.76711078704-0.133576821510.135460283887-0.436441606691-0.1898055314610.0833221056193-0.191397476150.1169739389910.125118941105-0.02013622572860.234372386324-0.03065852731810.04132218031810.165772935769-0.02986233980860.194771109617108.53377878530.760559476421.6395903287
22.39016672639-1.14552711224-0.8553585036074.49193565027-0.02808503722631.296837847660.0005493339196920.003911514939830.0962736409452-0.0884050221173-0.0813619590485-0.3654654362360.1177611191590.05600268225130.06937395976520.208614777523-0.0224177324820.04858360361460.1737648187020.03214530733480.22336571150795.08593485910.522974761740.5965241172
31.81027608477-0.2136335693850.3245883997391.51799203333-0.2215012987891.91169737071-0.09773683690690.115419354663-0.105232857651-0.117032132660.03209505943350.147940896567-0.0120300461338-0.1669637625740.07084736197880.205294434697-0.03201813688670.01493106243830.163226232829-0.01922894113470.15525345603592.849463155330.194244913821.4110190093
43.57551123649-1.828111664260.5489179944963.81183734441-0.04920979090432.30965087495-0.204519423082-0.165294942884-0.0008347128483030.4709361008590.06890248343960.01396193299480.0379956487167-0.01314541349990.1248596412290.27982966724-0.01220862212970.002974484892550.228906779243-0.005485893549510.16080501222599.208664687846.181062285146.6186144429
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 118 )AA29 - 1181 - 90
22chain 'A' and (resid 119 through 291 )AA119 - 29191 - 254
33chain 'B' and (resid 24 through 118 )BD24 - 1181 - 85
44chain 'B' and (resid 119 through 290 )BD119 - 29086 - 257

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