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- PDB-8suk: Structure of Rhodococcus sp. USK13 DarR-c-di-AMP complex -

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Basic information

Entry
Database: PDB / ID: 8suk
TitleStructure of Rhodococcus sp. USK13 DarR-c-di-AMP complex
Components
  • DNA (5'-D(*AP*A)-3')
  • DarR
KeywordsTRANSCRIPTION / TFR / Mycobacteria
Function / homologyDNA
Function and homology information
Biological speciesRhodococcus sp. USK13 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 12, 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.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DarR
B: DarR
C: DarR
D: DarR
J: DNA (5'-D(*AP*A)-3')
K: DNA (5'-D(*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,60512
Polymers95,0296
Non-polymers5766
Water3,153175
1
A: DarR
C: DarR
K: DNA (5'-D(*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8026
Polymers47,5143
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DarR
D: DarR
J: DNA (5'-D(*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8026
Polymers47,5143
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.542, 38.981, 115.641
Angle α, β, γ (deg.)90.00, 91.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DarR


Mass: 23466.424 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. USK13 (bacteria) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(*AP*A)-3')


Mass: 581.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 274 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 1.34 M lithium sulphate and 1.3% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→41.49 Å / Num. obs: 40140 / % possible obs: 98 % / Redundancy: 3.2 % / CC1/2: 0.989 / Rpim(I) all: 0.07 / Rsym value: 0.107 / Net I/σ(I): 5.8
Reflection shellResolution: 2.45→2.52 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2175 / CC1/2: 0.654 / Rpim(I) all: 0.378 / Rsym value: 0.538

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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: 2.45→41.49 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 2006 5 %
Rwork0.2146 --
obs0.2169 40140 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6052 78 30 176 6336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.939
X-RAY DIFFRACTIONf_dihedral_angle_d8.742909
X-RAY DIFFRACTIONf_chiral_restr0.049980
X-RAY DIFFRACTIONf_plane_restr0.0091100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.41961130.37772114X-RAY DIFFRACTION78
2.51-2.580.39481470.33072650X-RAY DIFFRACTION95
2.58-2.660.3171420.2962715X-RAY DIFFRACTION99
2.66-2.740.33111370.25822730X-RAY DIFFRACTION99
2.74-2.840.28461460.25462739X-RAY DIFFRACTION99
2.84-2.950.33171380.26442765X-RAY DIFFRACTION100
2.95-3.090.3181440.26922741X-RAY DIFFRACTION100
3.09-3.250.31961480.24532793X-RAY DIFFRACTION100
3.25-3.450.24551470.22552740X-RAY DIFFRACTION100
3.45-3.720.24821440.21542781X-RAY DIFFRACTION100
3.72-4.090.26411470.18492774X-RAY DIFFRACTION100
4.09-4.680.23051470.1742793X-RAY DIFFRACTION99
4.68-5.90.22891530.19512837X-RAY DIFFRACTION100
5.9-100.21251530.18522962X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.0161 Å / Origin y: -9.2999 Å / Origin z: 58.5224 Å
111213212223313233
T0.3295 Å20.0181 Å2-0.0065 Å2-0.3296 Å2-0.0055 Å2--0.4617 Å2
L0.5289 °20.0539 °2-0.0873 °2-0.5252 °2-0.4769 °2--3.3813 °2
S-0.0533 Å °0.019 Å °-0.0264 Å °0.002 Å °0.1463 Å °0.138 Å °0.0282 Å °-0.639 Å °-0.1087 Å °
Refinement TLS groupSelection details: all

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