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- PDB-7w07: Itaconate inducible LysR-Type Transcriptional regulator (ITCR) in... -

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Basic information

Entry
Database: PDB / ID: 7w07
TitleItaconate inducible LysR-Type Transcriptional regulator (ITCR) in complex with itaconate, Space group C121.
ComponentsTranscriptional regulator, LysR family
KeywordsTRANSCRIPTION / LTTR / ITCR / itaconate
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
HTH-type transcriptional regulator BudR, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
2-methylidenebutanedioic acid / Transcriptional regulator, LysR family
Similarity search - Component
Biological speciesYersinia pseudotuberculosis serotype O:3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsSun, P.K. / Wang, B. / Li, X.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073060 China
CitationJournal: Nat Commun / Year: 2022
Title: A genetically encoded fluorescent biosensor for detecting itaconate with subcellular resolution in living macrophages.
Authors: Sun, P. / Zhang, Z. / Wang, B. / Liu, C. / Chen, C. / Liu, P. / Li, X.
History
DepositionNov 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4843
Polymers32,2581
Non-polymers2262
Water3,045169
1
A: Transcriptional regulator, LysR family
hetero molecules

A: Transcriptional regulator, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9686
Polymers64,5162
Non-polymers4524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2510 Å2
ΔGint-37 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.772, 52.579, 49.183
Angle α, β, γ (deg.)90.000, 123.320, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

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Components

#1: Protein Transcriptional regulator, LysR family


Mass: 32258.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis serotype O:3 (strain YPIII) (bacteria)
Strain: YPIII / Gene: YPK_2265 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3B558
#2: Chemical ChemComp-ITN / 2-methylidenebutanedioic acid


Mass: 130.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.45 Å3/Da / Density % sol: 15.36 %
Crystal growTemperature: 276 K / Method: evaporation
Details: 1.6M Ammonium sulfate, 0.1M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.48→42.57 Å / Num. obs: 27190 / % possible obs: 87.3 % / Redundancy: 12.4 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.014 / Rrim(I) all: 0.052 / Net I/σ(I): 27 / Num. measured all: 338461
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.48-1.558.50.691821121460.8790.2440.7352.547.5
4.66-42.5712.90.02413154101810.0070.02486.199.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18_3855refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W06

7w06


Resolution: 1.48→41.1 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 1375 5.06 %
Rwork0.1785 25795 -
obs0.1793 27170 87.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.73 Å2 / Biso mean: 23.4514 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 1.48→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 14 169 1744
Biso mean--24.09 29.62 -
Num. residues----205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.530.2371570.23291327138445
1.53-1.590.2233950.2151724181959
1.59-1.660.20921140.20852480259484
1.66-1.750.18521340.19332840297495
1.75-1.860.2241700.18742798296896
1.86-20.19761510.18532897304897
2-2.20.18181230.18212943306698
2.2-2.520.2051860.18482878306498
2.52-3.180.21651490.18382952310199
3.18-41.10.17511960.16082956315298

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