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- PDB-8sua: Structure of M. baixiangningiae DarR-ligand complex -

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Basic information

Entry
Database: PDB / ID: 8sua
TitleStructure of M. baixiangningiae DarR-ligand complex
ComponentsDarR
KeywordsTRANSCRIPTION / DarR / mycobacteria / TFR / TetR / c-di-AMP
Function / homologyChem-YT9
Function and homology information
Biological speciesMycobacteriaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7042
Polymers23,4841
Non-polymers2201
Water3,351186
1
A: DarR
hetero molecules

A: DarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4094
Polymers46,9692
Non-polymers4402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2640 Å2
ΔGint-19 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.437, 85.437, 62.436
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-580-

HOH

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Components

#1: Protein DarR


Mass: 23484.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteriaceae (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-YT9 / 3-azanyl-3-(hydroxymethyl)-1,5,7,11-tetraoxa-6$l^{4}-boraspiro[5.5]undecan-9-ol


Mass: 220.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15BNO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: 1.5 M NaCl, 0.2 M MgCl2, 0.1 M Tris

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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 PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.72 Å / Num. obs: 35029 / % possible obs: 99.9 % / Redundancy: 11.2 % / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.047 / Net I/σ(I): 25.2
Reflection shellResolution: 1.6→1.64 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2647 / CC1/2: 0.805 / Rpim(I) all: 0.406 / Rsym value: 0.503

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→47.72 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1775 5.07 %
Rwork0.1841 --
obs0.1853 35029 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 15 186 1710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.15
X-RAY DIFFRACTIONf_dihedral_angle_d4.126234
X-RAY DIFFRACTIONf_chiral_restr0.055238
X-RAY DIFFRACTIONf_plane_restr0.012269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.23531350.20162517X-RAY DIFFRACTION99
1.64-1.690.23651300.19362503X-RAY DIFFRACTION100
1.69-1.750.27111370.23222559X-RAY DIFFRACTION100
1.75-1.810.23311340.20052512X-RAY DIFFRACTION100
1.81-1.880.19921360.18932528X-RAY DIFFRACTION100
1.88-1.970.19631320.18212558X-RAY DIFFRACTION100
1.97-2.070.19991370.17752536X-RAY DIFFRACTION100
2.07-2.20.23851370.19042555X-RAY DIFFRACTION100
2.2-2.370.19651340.17082555X-RAY DIFFRACTION100
2.37-2.610.18651390.18092568X-RAY DIFFRACTION100
2.61-2.990.2281360.19342566X-RAY DIFFRACTION100
2.99-3.760.20941400.17662597X-RAY DIFFRACTION100
3.76-100.19491480.18032700X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.8114 Å / Origin y: 41.4852 Å / Origin z: 19.8965 Å
111213212223313233
T0.179 Å20.0197 Å2-0.0054 Å2-0.1372 Å20.0071 Å2--0.1407 Å2
L0.8255 °21.0316 °20.421 °2-2.1948 °20.9827 °2--0.7027 °2
S0.0016 Å °-0.0077 Å °-0.0214 Å °-0.078 Å °-0.0494 Å °0.1132 Å °0.0857 Å °-0.0308 Å °0.0452 Å °
Refinement TLS groupSelection details: all

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