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- PDB-7w06: Itaconate inducible LysR-Type Transcriptional regulator (ITCR) in... -

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Basic information

Entry
Database: PDB / ID: 7w06
TitleItaconate inducible LysR-Type Transcriptional regulator (ITCR) in complex with itaconate (SeMet labeled), 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
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 / MAD / Resolution: 1.5 Å
AuthorsSun, P.K. / Wang, B. / Wang, Z.X. / Qi, S. / 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

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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)32,8954
Polymers32,6331
Non-polymers2623
Water2,828157
1
A: Transcriptional regulator, LysR family
hetero molecules

A: Transcriptional regulator, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7908
Polymers65,2662
Non-polymers5236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2720 Å2
ΔGint-50 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.766, 52.369, 49.079
Angle α, β, γ (deg.)90.000, 123.140, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

21A-556-

HOH

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Components

#1: Protein Transcriptional regulator, LysR family


Mass: 32633.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis serotype O:3 (strain YPIII) (bacteria)
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.43 Å3/Da / Density % sol: 14.02 %
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 5, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 52443 / % possible obs: 93.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.019 / Rrim(I) all: 0.046 / Χ2: 0.733 / Net I/σ(I): 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.553.20.08219100.9740.0520.0980.56165.2
1.55-1.623.70.07623270.9820.0440.0880.58579.5
1.62-1.694.40.0728840.9860.0360.0790.62697.3
1.69-1.785.10.06129330.9910.030.0680.69499.3
1.78-1.8960.05629480.9940.0250.0610.77699.8
1.89-2.045.90.0529130.9950.0220.0550.79599.1
2.04-2.2460.04529560.9940.020.0490.79899.6
2.24-2.5660.04329470.9940.0190.0470.77299.7
2.56-3.236.20.0429610.9960.0170.0430.7399.7
3.23-506.20.03930330.9960.0170.0420.7499.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18_3855refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→21.98 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 2580 4.92 %
Rwork0.1757 49863 -
obs0.1766 52443 90.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.3 Å2 / Biso mean: 15.0878 Å2 / Biso min: 4.05 Å2
Refinement stepCycle: final / Resolution: 1.5→21.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 15 157 1745
Biso mean--22.24 21.77 -
Num. residues----207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.530.2357760.2061487156348
1.53-1.560.22551440.18921745188960
1.56-1.590.25221110.19812102221369
1.59-1.630.2201950.19742556265182
1.63-1.670.24131550.19672909306496
1.67-1.720.19741490.18842980312997
1.72-1.770.18751490.18162940308996
1.77-1.820.19891640.18792985314998
1.82-1.890.18061620.17043049321199
1.89-1.960.21491400.18073007314798
1.96-2.050.22111540.16952951310597
2.05-2.160.17011690.16842979314898
2.16-2.30.16991670.17112989315697
2.3-2.470.19911480.1823028317698
2.47-2.720.20521740.18973006318099
2.72-3.120.21891550.1833022317799
3.12-3.920.17041180.16513088320699
3.92-21.980.17111500.15873040319099

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