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- PDB-6sbs: YtrA from Sulfolobus acidocaldarius, a GntR-family transcription ... -

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Basic information

Entry
Database: PDB / ID: 6sbs
TitleYtrA from Sulfolobus acidocaldarius, a GntR-family transcription factor
ComponentsRegulatory proteinRegulation of gene expression
KeywordsTRANSCRIPTION / transcription regulation / archaea / Sulfolobus / GntR / YtrA
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.801 Å
AuthorsLemmens, L. / Valegard, K. / Lindas, A.C. / Peeters, E. / Maes, D.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Other governmentG021118 Belgium
Other government1526418N Belgium
CitationJournal: Front Microbiol / Year: 2019
Title: YtrASa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins inSulfolobus acidocaldarius.
Authors: Lemmens, L. / Tilleman, L. / De Koning, E. / Valegard, K. / Lindas, A.C. / Van Nieuwerburgh, F. / Maes, D. / Peeters, E.
History
DepositionJul 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein
B: Regulatory protein


Theoretical massNumber of molelcules
Total (without water)27,8102
Polymers27,8102
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-24 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.090, 133.090, 39.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Regulatory protein / Regulation of gene expression


Mass: 13905.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: Saci_1851 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q4J7S4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.5 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20 % (w/v) 229 PEG3350, 0.2 M sodium nitrate and 0.1 M Bis-Tris propane, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.801→38.42 Å / Num. obs: 10103 / % possible obs: 100 % / Redundancy: 10.01 % / CC1/2: 0.995 / Rrim(I) all: 0.209 / Net I/σ(I): 8.88
Reflection shellResolution: 2.801→2.87 Å / Num. unique obs: 727 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.801→38.42 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.94
RfactorNum. reflection% reflection
Rfree0.3208 505 5 %
Rwork0.2489 --
obs0.2525 10092 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.56 Å2 / Biso mean: 74.0029 Å2 / Biso min: 23.34 Å2
Refinement stepCycle: final / Resolution: 2.801→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 0 66 1757
Biso mean---70.45 -
Num. residues----210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.801-3.08230.39831250.33982376
3.0823-3.5280.33761250.28172357
3.528-4.44390.27731260.22622395
4.4439-38.420.33371290.23972459

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