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- PDB-8tp8: Structure of the C. crescentus WYL-activator, DriD, bound to ssDN... -

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Basic information

Entry
Database: PDB / ID: 8tp8
TitleStructure of the C. crescentus WYL-activator, DriD, bound to ssDNA and cognate DNA
Components
  • DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*AP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
  • DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
  • DNA (5'-D(P*GP*TP*C)-3')
  • DeoR-family transcriptional regulator
KeywordsTRANSCRIPTION/DNA / WYL motif / DriD / C. crescentus / DNA damage repair / ssDNA / transcription activation / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homologyProtein PafC / WYL domain / WYL domain / DNA / DNA (> 10) / DeoR-family transcriptional regulator
Function and homology information
Biological speciesCaulobacter vibrioides NA1000 (bacteria)
Caulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site.
Authors: Schumacher, M.A. / Cannistraci, E. / Salinas, R. / Lloyd, D. / Messner, E. / Gozzi, K.
History
DepositionAug 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DeoR-family transcriptional regulator
B: DeoR-family transcriptional regulator
U: DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
R: DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*AP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
L: DNA (5'-D(P*GP*TP*C)-3')
Y: DNA (5'-D(P*GP*TP*C)-3')
C: DeoR-family transcriptional regulator
D: DeoR-family transcriptional regulator
J: DNA (5'-D(P*GP*TP*C)-3')
K: DNA (5'-D(P*GP*TP*C)-3')
F: DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
T: DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*AP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,00218
Polymers181,42612
Non-polymers5766
Water1,946108
1
A: DeoR-family transcriptional regulator
B: DeoR-family transcriptional regulator
U: DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
R: DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*AP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
L: DNA (5'-D(P*GP*TP*C)-3')
Y: DNA (5'-D(P*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9058
Polymers90,7136
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16770 Å2
ΔGint-126 kcal/mol
Surface area33340 Å2
MethodPISA
2
C: DeoR-family transcriptional regulator
D: DeoR-family transcriptional regulator
J: DNA (5'-D(P*GP*TP*C)-3')
K: DNA (5'-D(P*GP*TP*C)-3')
F: DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
T: DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*AP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,09710
Polymers90,7136
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17160 Å2
ΔGint-139 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.260, 178.941, 92.150
Angle α, β, γ (deg.)90.00, 95.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DeoR-family transcriptional regulator / DriD


Mass: 38037.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria)
Gene: CCNA_01151 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3C5Q6

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DNA chain , 3 types, 8 molecules UFRTLYJK

#2: DNA chain DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')


Mass: 6437.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Caulobacter vibrioides (bacteria)
#3: DNA chain DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*AP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')


Mass: 6446.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Caulobacter vibrioides (bacteria)
#4: DNA chain
DNA (5'-D(P*GP*TP*C)-3')


Mass: 877.623 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Caulobacter vibrioides (bacteria)

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Non-polymers , 2 types, 114 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, 1.0 M Citrate

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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 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→69 Å / Num. obs: 56088 / % possible obs: 96.1 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.06 / Net I/σ(I): 7.6
Reflection shellResolution: 2.74→2.89 Å / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3276 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→68.97 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 2000 3.57 %
Rwork0.1958 --
obs0.1975 56088 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→68.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9839 1954 30 108 11931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912259
X-RAY DIFFRACTIONf_angle_d1.15917032
X-RAY DIFFRACTIONf_dihedral_angle_d23.222362
X-RAY DIFFRACTIONf_chiral_restr0.0561895
X-RAY DIFFRACTIONf_plane_restr0.0071904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.810.36841170.3533150X-RAY DIFFRACTION79
2.81-2.890.39131410.32593814X-RAY DIFFRACTION94
2.89-2.970.35411450.3033923X-RAY DIFFRACTION99
2.97-3.070.34111440.28423922X-RAY DIFFRACTION98
3.07-3.180.31921470.26763964X-RAY DIFFRACTION98
3.18-3.30.3021460.23753947X-RAY DIFFRACTION98
3.3-3.450.26891420.21763834X-RAY DIFFRACTION96
3.45-3.640.27551460.20553946X-RAY DIFFRACTION98
3.64-3.860.25381460.19413961X-RAY DIFFRACTION99
3.86-4.160.21241410.17593804X-RAY DIFFRACTION95
4.16-4.580.19681460.16473973X-RAY DIFFRACTION98
4.58-5.240.22511470.16573962X-RAY DIFFRACTION99
5.24-6.610.2521440.19143921X-RAY DIFFRACTION97
6.61-68.970.1841480.16243967X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 29.1364 Å / Origin y: -16.2606 Å / Origin z: 45.204 Å
111213212223313233
T0.4579 Å2-0.0285 Å20.0435 Å2-0.468 Å2-0.0871 Å2--0.475 Å2
L0.8379 °2-0.1321 °20.4136 °2-0.3085 °2-0.2737 °2--0.9592 °2
S0.1009 Å °-0.0356 Å °-0.0617 Å °-0.0022 Å °-0.0042 Å °0.0226 Å °0.0202 Å °-0.2159 Å °-0.1131 Å °
Refinement TLS groupSelection details: all

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