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- PDB-5yej: Crystal structure of BioQ with its naturel double-stranded DNA op... -

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Basic information

Entry
Database: PDB / ID: 5yej
TitleCrystal structure of BioQ with its naturel double-stranded DNA operator
Components
  • DNA (5'-D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3')
  • DNA (5'-D(*AP*CP*TP*TP*GP*AP*AP*CP*GP*GP*TP*GP*TP*TP*CP*AP*GP*GP*T)-3')
  • TetR family transcriptional regulator
KeywordsDNA BINDING PROTEIN/DNA / BioQ / DNA complex / TetR family / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator, TetR family protein / Transcriptional regulator, TetR family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.698 Å
AuthorsYan, L. / Guan, Z.Y. / Zou, T.T.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2018
Title: Structural insights into operator recognition by BioQ in the Mycobacterium smegmatis biotin synthesis pathway.
Authors: Yan, L. / Tang, Q. / Guan, Z. / Pei, K. / Zou, T. / He, J.
History
DepositionSep 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Oct 10, 2018Group: Data collection / Derived calculations / Structure summary
Category: entity / pdbx_struct_assembly ...entity / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity.formula_weight
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
D: DNA (5'-D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3')
F: DNA (5'-D(*AP*CP*TP*TP*GP*AP*AP*CP*GP*GP*TP*GP*TP*TP*CP*AP*GP*GP*T)-3')
G: DNA (5'-D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3')
C: TetR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)92,9486
Polymers92,9486
Non-polymers00
Water724
1
A: TetR family transcriptional regulator
G: DNA (5'-D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3')

A: TetR family transcriptional regulator
G: DNA (5'-D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)61,8974
Polymers61,8974
Non-polymers00
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation1_255x-3,y,z1
crystal symmetry operation2_959-x+4,y,-z+41
2
B: TetR family transcriptional regulator
D: DNA (5'-D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3')
F: DNA (5'-D(*AP*CP*TP*TP*GP*AP*AP*CP*GP*GP*TP*GP*TP*TP*CP*AP*GP*GP*T)-3')
C: TetR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)61,9994
Polymers61,9994
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.687, 212.468, 88.126
Angle α, β, γ (deg.)90.00, 99.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-101-

HOH

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Components

#1: Protein TetR family transcriptional regulator / BioQ


Mass: 25174.936 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_3111 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I7FDJ0, UniProt: A0QX69*PLUS
#2: DNA chain DNA (5'-D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3')


Mass: 5773.763 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*TP*TP*GP*AP*AP*CP*GP*GP*TP*GP*TP*TP*CP*AP*GP*GP*T)-3')


Mass: 5875.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, magnesium acetate, 1-propanol, MOPS, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.69→45 Å / Num. obs: 29957 / % possible obs: 98 % / Redundancy: 7.3 % / Net I/σ(I): 7.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.698→37.676 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 1399 4.74 %
Rwork0.2116 --
obs0.2141 29496 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.698→37.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 1155 0 4 5011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095206
X-RAY DIFFRACTIONf_angle_d1.0747302
X-RAY DIFFRACTIONf_dihedral_angle_d28.2781925
X-RAY DIFFRACTIONf_chiral_restr0.06851
X-RAY DIFFRACTIONf_plane_restr0.005745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6978-2.79420.39221390.36212753X-RAY DIFFRACTION96
2.7942-2.9060.3931550.32892866X-RAY DIFFRACTION100
2.906-3.03820.36961580.28562836X-RAY DIFFRACTION99
3.0382-3.19830.31771470.25912803X-RAY DIFFRACTION99
3.1983-3.39860.31951220.24842732X-RAY DIFFRACTION95
3.3986-3.66080.31061340.2212731X-RAY DIFFRACTION95
3.6608-4.02880.24071440.20592836X-RAY DIFFRACTION98
4.0288-4.61090.25431440.19112834X-RAY DIFFRACTION99
4.6109-5.80590.23091230.22857X-RAY DIFFRACTION99
5.8059-37.67920.22381330.17992849X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 158.9312 Å / Origin y: 11.971 Å / Origin z: 189.4112 Å
111213212223313233
T0.8032 Å2-0.0946 Å2-0.199 Å2-0.6355 Å20.208 Å2--0.6484 Å2
L1.4131 °2-0.9435 °20.0691 °2-2.7487 °20.8327 °2--0.3075 °2
S-0.1166 Å °-0.1452 Å °0.054 Å °-0.0682 Å °0.0308 Å °0.1838 Å °-0.0773 Å °0.0086 Å °0.0696 Å °
Refinement TLS groupSelection details: all

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