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- PDB-8svd: Structure of M. baixiangningiae DarR-DNA complex reveals novel di... -

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Basic information

Entry
Database: PDB / ID: 8svd
TitleStructure of M. baixiangningiae DarR-DNA complex reveals novel dimer-of-dimers DNA binding
Components
  • DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
  • DarR
KeywordsTRANSCRIPTION/DNA / DarR / repressor / transcription / TFR / TetR / QacR / dimer-of-dimers DNA binding / Mycobacteria / TRANSCRIPTION-DNA complex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesMycolicibacterium baixiangningiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM130290 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding.
Authors: Schumacher, M.A. / Lent, N. / Chen, V.B. / Salinas, R.
History
DepositionMay 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
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 / _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: DarR
F: DarR
G: DarR
T: DarR
D: DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
B: DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
E: DarR
I: DarR
J: DarR
K: DarR
M: DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
Q: DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)212,03912
Polymers212,03912
Non-polymers00
Water00
1
A: DarR
F: DarR
G: DarR
T: DarR
D: DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
B: DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)106,0206
Polymers106,0206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-101 kcal/mol
Surface area40310 Å2
MethodPISA
2
E: DarR
I: DarR
J: DarR
K: DarR
M: DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')
Q: DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)106,0206
Polymers106,0206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-101 kcal/mol
Surface area40920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.034, 155.758, 117.844
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DarR


Mass: 23438.436 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium baixiangningiae (bacteria)
Production host: Escherichia coli (E. coli)
#2: DNA chain
DNA (5'-D(P*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')


Mass: 6132.991 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Mycolicibacterium baixiangningiae (bacteria)

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.0, 0.2 M magnesium chloride and 13% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.49→47.45 Å / Num. obs: 30500 / % possible obs: 98.4 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rpim(I) all: 0.061 / Rsym value: 0.095 / Net I/σ(I): 5.2
Reflection shellResolution: 3.49→3.58 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2100 / CC1/2: 0.868 / Rpim(I) all: 0.253 / Rsym value: 0.402

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→47.45 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2844 1998 6.55 %
Rwork0.2669 --
obs0.268 30500 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.49→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11829 1575 0 0 13404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.823
X-RAY DIFFRACTIONf_dihedral_angle_d21.9035021
X-RAY DIFFRACTIONf_chiral_restr0.0472186
X-RAY DIFFRACTIONf_plane_restr0.0042205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.580.40791480.38352098X-RAY DIFFRACTION100
3.58-3.670.38181400.35772014X-RAY DIFFRACTION99
3.67-3.780.371460.34642080X-RAY DIFFRACTION100
3.78-3.90.35171430.33482027X-RAY DIFFRACTION100
3.9-4.040.36541440.30082054X-RAY DIFFRACTION99
4.04-4.210.33141440.30392053X-RAY DIFFRACTION99
4.21-4.40.35121430.29382030X-RAY DIFFRACTION99
4.4-4.630.28991430.27522046X-RAY DIFFRACTION99
4.63-4.920.29581430.27322037X-RAY DIFFRACTION98
4.92-5.30.2751430.27022035X-RAY DIFFRACTION98
5.3-5.830.29211400.28852011X-RAY DIFFRACTION98
5.83-6.670.30291410.28962023X-RAY DIFFRACTION97
6.67-8.40.26061390.261990X-RAY DIFFRACTION95
8-100.19361410.18062004X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 32.4047 Å / Origin y: -8.8571 Å / Origin z: -23.3393 Å
111213212223313233
T1.3128 Å2-0.0201 Å2-0.0181 Å2-0.6323 Å20.0354 Å2--0.749 Å2
L0.1959 °2-0.18 °2-0.2327 °2-0.5659 °20.0533 °2--1.6897 °2
S-0.1277 Å °-0.0733 Å °0.0019 Å °0.5816 Å °0.0993 Å °-0.0302 Å °-0.1399 Å °-0.158 Å °0.0448 Å °
Refinement TLS groupSelection details: all

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