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- PDB-8gyz: Crystal structure of transcription factor TGA7 from Arabidopsis -

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Basic information

Entry
Database: PDB / ID: 8gyz
TitleCrystal structure of transcription factor TGA7 from Arabidopsis
ComponentsTranscription factor TGA7
KeywordsDNA BINDING PROTEIN / TGA7-palmitate complex / transcription factor
Function / homology
Function and homology information


transcription cis-regulatory region binding / defense response to bacterium / DNA-binding transcription factor activity / nucleus
Similarity search - Function
Transcription factor TGA like domain / Seed dormancy control / DOG1 domain profile. / bZIP transcription factor / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
PALMITIC ACID / Transcription factor TGA7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsShi, X.Q. / Che, Z. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of transcription factor TGA7 from Arabidopsis.
Authors: Shi, X. / Che, Z. / Xu, G. / Ming, Z.
History
DepositionSep 24, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor TGA7
B: Transcription factor TGA7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0314
Polymers69,5182
Non-polymers5132
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-34 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.755, 85.840, 89.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription factor TGA7 / bZIP transcription factor 50 / AtbZIP50


Mass: 34759.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TGA7, BZIP50, At1g77920, F28K19.13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93ZE2
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.005M magnesium sulfate heptahydrate, 0.05 M MES monohydrate pH 6.0, 5% w/v polyethylene glycol 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30% v/v Polyethylene glycol 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.06→61.94 Å / Num. obs: 59814 / % possible obs: 91.9 % / Redundancy: 10 % / Biso Wilson estimate: 44.14 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.1
Reflection shellResolution: 2.06→2.17 Å / Num. unique obs: 4419 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
autoPROCdata scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q93ZE2-F1

Resolution: 2.06→55.942 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.95 / Stereochemistry target values: ML
Details: Author stated that 30% residues at N-terminal were in a highly flexible state, in which their electron densities could not be traced by X-ray diffraction.
RfactorNum. reflection% reflection
Rfree0.2216 3461 6.03 %
Rwork0.1819 56205 -
obs0.1843 59814 88.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.53 Å2 / Biso mean: 44.0542 Å2 / Biso min: 18.24 Å2
Refinement stepCycle: final / Resolution: 2.06→55.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 36 145 3609
Biso mean--37.07 43.74 -
Num. residues----427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.06-2.08670.33891120.2831187477
2.0867-2.11520.30711280.2655190677
2.1152-2.14550.32891120.2574195879
2.1455-2.17750.25731220.2392193078
2.1775-2.21150.26361260.2349189278
2.2115-2.24780.2571610.2257100769
2.2478-2.28650.2546820.2223126576
2.2865-2.32810.2871460.2225215088
2.3281-2.37290.2691430.2237238696
2.3729-2.42130.22941500.2131234397
2.4213-2.4740.2511500.2076236696
2.474-2.53150.24831530.2012237897
2.5315-2.59480.23771490.1896240798
2.5948-2.6650.24021550.1959240498
2.665-2.74340.25011610.1791242099
2.7434-2.83190.19271580.1784246499
2.8319-2.93320.21191490.1873239799
2.9332-3.05060.211580.1879244999
3.0506-3.18940.241640.1818240799
3.1894-3.35760.22111540.1737242299
3.3576-3.56790.22761500.1765236396
3.5679-3.84330.17551000.1502144459
3.8433-4.22990.24541420.1497236196
4.2299-4.84170.18861530.1483240898
4.8417-6.09890.22081630.1852240899
6.0989-55.9420.17271680.1692239698
Refinement TLS params.Method: refined / Origin x: 5.3116 Å / Origin y: -6.6517 Å / Origin z: -25.0632 Å
111213212223313233
T0.1995 Å20.0102 Å20.0118 Å2-0.2354 Å2-0.0341 Å2--0.21 Å2
L0.5403 °2-0.6687 °20.7173 °2-1.431 °2-1.2613 °2--1.2059 °2
S0.1281 Å °0.1191 Å °-0.053 Å °-0.1672 Å °-0.0892 Å °0.0822 Å °0.1161 Å °0.1574 Å °-0.0339 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA149 - 360
2X-RAY DIFFRACTION1allB151 - 365
3X-RAY DIFFRACTION1allS1 - 145
4X-RAY DIFFRACTION1allC501
5X-RAY DIFFRACTION1allD401

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