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- PDB-8ejv: The crystal structure of Pseudomonas putida PcaR in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8ejv
TitleThe crystal structure of Pseudomonas putida PcaR in complex with succinate
ComponentsTranscription regulatory protein (Pca regulon)
KeywordsTRANSCRIPTION / Complex / Transcription Factor / Succinate / 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 / SUCCINIC ACID / Transcription regulatory protein (Pca regulon)
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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)64,0569
Polymers63,5572
Non-polymers5007
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-61 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.822, 148.822, 56.650
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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 137 molecules

#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Reservoir: 1.8 M ammonium phosphate monophosphate, 0.1 M succinic acid, pH 7, 1.25% w/v Benzyltriethylammonium chloride

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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: Aug 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.925 Å / Relative weight: 1
ReflectionResolution: 2.43→37.21 Å / Num. obs: 26706 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 58.04 Å2 / CC1/2: 1 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Net I/σ(I): 56.16
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 1243 / CC1/2: 0.906 / Rpim(I) all: 0.193 / Rrim(I) all: 0.628

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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: 2.43→37.21 Å / SU ML: 0.2918 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1337 5.01 %RANDOM
Rwork0.2083 25369 --
obs0.2107 26706 97.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.26 Å2
Refinement stepCycle: LAST / Resolution: 2.43→37.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 28 130 4077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054013
X-RAY DIFFRACTIONf_angle_d0.81315440
X-RAY DIFFRACTIONf_chiral_restr0.0488642
X-RAY DIFFRACTIONf_plane_restr0.0072703
X-RAY DIFFRACTIONf_dihedral_angle_d16.05321492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.510.31121310.28422523X-RAY DIFFRACTION98.99
2.52-2.620.33451340.26212580X-RAY DIFFRACTION99.52
2.62-2.730.34761320.26552562X-RAY DIFFRACTION99.45
2.73-2.880.28731350.23972572X-RAY DIFFRACTION99.82
2.88-3.060.30291330.24512584X-RAY DIFFRACTION99.74
3.06-3.30.29551370.22632568X-RAY DIFFRACTION99.74
3.3-3.630.26871330.22462520X-RAY DIFFRACTION97.14
3.63-4.150.22871190.19792165X-RAY DIFFRACTION83.21
4.15-5.230.20741360.16732619X-RAY DIFFRACTION99.78
5.23-37.210.24431470.19632676X-RAY DIFFRACTION99.79
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)
15.78903033109-0.79074185126-1.065442958742.12918223392-0.5034024338293.91533587468-0.294382973576-0.257560717193-0.5487883427720.2214219117430.278222046030.2602771579560.241544006626-0.427648179249-0.02127082519690.4829834263680.08761763273010.1002760059230.3506297514280.07886906151390.431385597240.381939344830.916107700818.0707121018
23.702301198271.6004561907-0.6207921536256.16494305540.05301026799582.56724114139-0.05689214434970.162824344033-0.0986696956780.176942757955-0.1343487762660.339519406790.3830118328-0.1206283542050.2006920171590.4220291732870.06110855725230.127625838460.306725776285-0.04788116621850.41373242096253.838200859210.7529993001-1.12556706676
35.398109652530.8016461601642.272266932084.12224199289-0.649599589134.60304116308-0.121538947366-0.202162685208-0.187544026910.197086353369-0.108019813605-0.33135920465-0.3584991215120.4456185881040.2141186096890.5031351919590.05537282042230.03369962737040.4065032728060.05074105275580.34707088571855.446606740331.920043631819.2512941772
43.903876628032.69555752424-0.6166408788696.34962528720.006745274861655.62396668555-0.2644858045520.273683227214-0.579240968695-0.9628148097750.0799600406538-0.3619049846890.5372897523820.3345325791930.1200509553670.5761866679510.04123208019110.05684218652070.3571321792320.01469836507240.41060986467149.973651472338.2882342074-5.43045180999
56.290711659322.502180409231.039155291295.479229593660.8648196453914.94392382412-0.2349231950640.2666632227470.388037962794-0.7033450144720.0769806326230.127481531583-0.317629123054-0.01073558149470.1584403368080.5368033143690.0128400285875-0.02460406699440.3782957436190.06022277532710.38444988066249.477790542850.6172196467-7.58535659327
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 - 255
33chain 'B' and (resid 41 through 118 )BD41 - 1181 - 78
44chain 'B' and (resid 119 through 177 )BD119 - 17779 - 137
55chain 'B' and (resid 178 through 291 )BD178 - 291138 - 251

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