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- PDB-7eqf: Crystal Structure of a Transcription Factor in complex with Ligand -

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Basic information

Entry
Database: PDB / ID: 7eqf
TitleCrystal Structure of a Transcription Factor in complex with Ligand
ComponentsTetR/AcrR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription Factor
Function / homology
Function and homology information


regulation of gene expression / DNA binding
Similarity search - Function
DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Chem-JB0 / TetR/AcrR family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces griseoluteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.91 Å
AuthorsUehara, S. / Tsugita, A. / Matsui, T. / Yokoyama, T. / Ostash, I. / Ostash, B. / Tanaka, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Febs J. / Year: 2022
Title: The carbohydrate tail of landomycin A is responsible for its interaction with the repressor protein LanK.
Authors: Tsugita, A. / Uehara, S. / Matsui, T. / Yokoyama, T. / Ostash, I. / Deneka, M. / Yalamanchili, S. / Bennett, C.S. / Tanaka, Y. / Ostash, B.
History
DepositionMay 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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: TetR/AcrR family transcriptional regulator
B: TetR/AcrR family transcriptional regulator
C: TetR/AcrR family transcriptional regulator
D: TetR/AcrR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6037
Polymers89,3424
Non-polymers3,2613
Water00
1
A: TetR/AcrR family transcriptional regulator
B: TetR/AcrR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7583
Polymers44,6712
Non-polymers1,0871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-14 kcal/mol
Surface area18030 Å2
MethodPISA
2
C: TetR/AcrR family transcriptional regulator
D: TetR/AcrR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8454
Polymers44,6712
Non-polymers2,1742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-19 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.469, 53.556, 109.978
Angle α, β, γ (deg.)90.000, 95.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TetR/AcrR family transcriptional regulator


Mass: 22335.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoluteus (bacteria) / Gene: E5082_18205 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Z1DIH6
#2: Chemical ChemComp-JB0 / (6~{R})-3-methyl-8-[(2~{S},4~{R},5~{S},6~{R})-6-methyl-5-[(2~{S},4~{R},5~{R},6~{R})-6-methyl-4-[(2~{S},5~{S},6~{S})-6-methyl-5-[(2~{S},4~{R},5~{S},6~{R})-6-methyl-5-[(2~{S},4~{S},5~{S},6~{R})-6-methyl-4-[(2~{S},5~{S},6~{S})-6-methyl-5-oxidanyl-oxan-2-yl]oxy-5-oxidanyl-oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-oxan-2-yl]oxy-5-oxidanyl-oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-1,6,11-tris(oxidanyl)-5,6-dihydrobenzo[a]anthracene-7,12-dione


Mass: 1087.163 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H74O22 / Feature type: SUBJECT OF INVESTIGATION
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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: HEPES-NaOH pH 7.5, polyethylene glycol 4000, isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.977945 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977945 Å / Relative weight: 1
ReflectionResolution: 2.91→47.73 Å / Num. obs: 40256 / % possible obs: 96.8 % / Redundancy: 3.42 % / Biso Wilson estimate: 76.41 Å2 / Rsym value: 0.134 / Net I/σ(I): 8.69
Reflection shellResolution: 2.91→3.08 Å / Num. unique obs: 5721 / Rsym value: 0.922

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EQE

7eqe


Resolution: 2.91→47.73 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 3205 7.97 %
Rwork0.2476 37025 -
obs0.249 40230 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 218.89 Å2 / Biso mean: 76.0306 Å2 / Biso min: 37.6 Å2
Refinement stepCycle: final / Resolution: 2.91→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 159 0 5625
Biso mean--87.99 --
Num. residues----705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.91-2.950.42591070.46831234134174
2.95-30.4221240.42451428155285
3-3.050.44261300.39741481161189
3.05-3.10.371370.35161554169195
3.1-3.160.37011470.33711682182999
3.16-3.220.33531450.313516331778100
3.22-3.280.38021400.29891653179399
3.28-3.350.30741410.304217271868100
3.35-3.430.34761390.30081587172699
3.43-3.520.35051460.31311670181699
3.52-3.610.35531440.281816631807100
3.61-3.720.30551420.26681610175299
3.72-3.840.25351510.25041714186599
3.84-3.980.24221440.2371586173099
3.98-4.130.27061480.22771649179799
4.13-4.320.27131370.227716441781100
4.32-4.550.23331440.21781658180299
4.55-4.840.20151450.21921666181199
4.84-5.210.23951430.22941637178099
5.21-5.730.32251300.24321614174498
5.73-6.560.33131450.25471644178999
6.56-8.260.20941400.19731665180599
8.26-47.730.14441360.18391626176297

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