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- PDB-6en8: SaFadR in complex with dsDNA -

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Basic information

Entry
Database: PDB / ID: 6en8
TitleSaFadR in complex with dsDNA
Components
  • DNA (5'-D(*CP*TP*AP*CP*TP*TP*GP*AP*TP*TP*TP*TP*TP*GP*AP*GP*TP*CP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*GP*AP*CP*TP*CP*AP*AP*AP*AP*AP*TP*CP*AP*AP*GP*TP*AP*G)-3')
  • Transcriptional regulator TetR family
KeywordsTRANSCRIPTION / transcription factor / complex / dsDNA
Function / homology
Function and homology information


: / 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / DNA / DNA (> 10) / Transcriptional regulator TetR family
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsValegard, K.
CitationJournal: Nat Commun / Year: 2019
Title: A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.
Authors: Wang, K. / Sybers, D. / Maklad, H.R. / Lemmens, L. / Lewyllie, C. / Zhou, X. / Schult, F. / Brasen, C. / Siebers, B. / Valegard, K. / Lindas, A.C. / Peeters, E.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator TetR family
B: Transcriptional regulator TetR family
C: Transcriptional regulator TetR family
D: Transcriptional regulator TetR family
E: Transcriptional regulator TetR family
F: Transcriptional regulator TetR family
Q: DNA (5'-D(*GP*TP*CP*GP*AP*CP*TP*CP*AP*AP*AP*AP*AP*TP*CP*AP*AP*GP*TP*AP*G)-3')
X: DNA (5'-D(*CP*TP*AP*CP*TP*TP*GP*AP*TP*TP*TP*TP*TP*GP*AP*GP*TP*CP*GP*AP*C)-3')
Y: DNA (5'-D(*GP*TP*CP*GP*AP*CP*TP*CP*AP*AP*AP*AP*AP*TP*CP*AP*AP*GP*TP*AP*G)-3')
Z: DNA (5'-D(*CP*TP*AP*CP*TP*TP*GP*AP*TP*TP*TP*TP*TP*GP*AP*GP*TP*CP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,76512
Polymers168,23010
Non-polymers1,5352
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26040 Å2
ΔGint-224 kcal/mol
Surface area61300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.850, 178.310, 266.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transcriptional regulator TetR family / FadR transcription factor


Mass: 23687.121 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: Saci_1107 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9S1
#2: DNA chain DNA (5'-D(*GP*TP*CP*GP*AP*CP*TP*CP*AP*AP*AP*AP*AP*TP*CP*AP*AP*GP*TP*AP*G)-3')


Mass: 6549.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*TP*AP*CP*TP*TP*GP*AP*TP*TP*TP*TP*TP*GP*AP*GP*TP*CP*GP*AP*C)-3')


Mass: 6504.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically
Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8, 0.4M Lithium chloride, 15% PEG 6000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.29→49.41 Å / Num. obs: 40698 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 68.53 Å2 / CC1/2: 0.958 / Rrim(I) all: 0.095 / Net I/σ(I): 12.59
Reflection shellResolution: 3.29→3.38 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 2851 / CC1/2: 0.953 / Rrim(I) all: 0.746 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MWR

5mwr
PDB Unreleased entry


Resolution: 3.29→49.41 Å / Cor.coef. Fo:Fc: 0.9044 / Cor.coef. Fo:Fc free: 0.8833 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.402
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 2035 5 %RANDOM
Rwork0.2019 ---
obs0.2037 40699 99.47 %-
Displacement parametersBiso mean: 139.76 Å2
Baniso -1Baniso -2Baniso -3
1--43.594 Å20 Å20 Å2
2---13.4938 Å20 Å2
3---57.0878 Å2
Refine analyzeLuzzati coordinate error obs: 0.975 Å
Refinement stepCycle: 1 / Resolution: 3.29→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9345 1713 73 0 11131
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811532HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9115884HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3950SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1452HARMONIC5
X-RAY DIFFRACTIONt_it11532HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion22.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1483SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12808SEMIHARMONIC4
LS refinement shellResolution: 3.29→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2737 140 4.98 %
Rwork0.2531 2673 -
all0.2541 2813 -
obs--99.47 %

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