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- PDB-7w08: Itaconate inducible LysR-Type Transcriptional regulator (ITCR) in... -

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Basic information

Entry
Database: PDB / ID: 7w08
TitleItaconate inducible LysR-Type Transcriptional regulator (ITCR) in APO form, Space group P1.
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
Transcriptional regulator, LysR family
Similarity search - Component
Biological speciesYersinia pseudotuberculosis serotype O:3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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
C: Transcriptional regulator, LysR family
D: Transcriptional regulator, LysR family
A: Transcriptional regulator, LysR family
B: Transcriptional regulator, LysR family
E: Transcriptional regulator, LysR family
F: Transcriptional regulator, LysR family
G: Transcriptional regulator, LysR family
H: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)258,0648
Polymers258,0648
Non-polymers00
Water00
1
C: Transcriptional regulator, LysR family
D: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)64,5162
Polymers64,5162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-15 kcal/mol
Surface area17390 Å2
MethodPISA
2
A: Transcriptional regulator, LysR family
B: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)64,5162
Polymers64,5162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-16 kcal/mol
Surface area17590 Å2
MethodPISA
3
E: Transcriptional regulator, LysR family
F: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)64,5162
Polymers64,5162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-15 kcal/mol
Surface area17590 Å2
MethodPISA
4
G: Transcriptional regulator, LysR family
H: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)64,5162
Polymers64,5162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-16 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.586, 73.519, 104.035
Angle α, β, γ (deg.)94.240, 105.670, 111.130
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Transcriptional regulator, LysR family


Mass: 32258.045 Da / Num. of mol.: 8
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

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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: 1.79 Å3/Da / Density % sol: 31.37 %
Crystal growTemperature: 276 K / Method: evaporation
Details: 0.2M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 25827 / % possible obs: 91.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.099 / Rrim(I) all: 0.192 / Χ2: 0.674 / Net I/σ(I): 3.8 / Num. measured all: 95622
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.373.40.56624600.7530.3530.6690.46886.9
3.37-3.53.70.46326400.8240.2780.5410.53495.1
3.5-3.663.70.33226420.8850.1980.3870.55993.4
3.66-3.853.80.24526300.9440.1460.2850.56993.1
3.85-4.093.70.20324770.9450.1220.2380.66688.4
4.09-4.413.70.14226070.9730.0850.1660.67793.6
4.41-4.853.80.11226410.9840.0660.130.72993.4
4.85-5.563.70.10824900.9860.0640.1260.69488.8
5.56-73.80.10726800.9860.0630.1250.68395.5
7-503.60.07125600.9920.0430.0831.14890.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18_3855refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W06

7w06


Resolution: 3.25→32.96 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1996 7.74 %
Rwork0.1991 23779 -
obs0.2021 25775 91.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.54 Å2 / Biso mean: 44.868 Å2 / Biso min: 12.44 Å2
Refinement stepCycle: final / Resolution: 3.25→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12189 0 0 0 12189
Num. residues----1643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.25-3.330.31021250.2631481160680
3.33-3.420.28361440.24721723186793
3.42-3.520.28911500.24851781193195
3.52-3.630.31251460.23081741188794
3.63-3.760.27851440.21711713185793
3.76-3.910.23331430.20651697184092
3.91-4.090.23161390.19751662180188
4.09-4.310.21581450.1871726187192
4.31-4.580.20581460.18271744189094
4.58-4.930.20221470.16861747189493
4.93-5.420.24171350.19481609174488
5.42-6.20.29751500.22341785193595
6.2-7.80.24341420.19881695183792
7.8-32.960.16751400.14541675181590

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