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- PDB-8tpk: P6522 crystal form of C. crescentus DriD-ssDNA-DNA complex -

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Basic information

Entry
Database: PDB / ID: 8tpk
TitleP6522 crystal form of C. crescentus DriD-ssDNA-DNA complex
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 / DriD / DNA repair / ssDNA / .c crescentus / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 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
L: DNA (5'-D(P*GP*TP*C)-3')
Y: DNA (5'-D(P*GP*TP*C)-3')
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')


Theoretical massNumber of molelcules
Total (without water)90,7136
Polymers90,7136
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15950 Å2
ΔGint-82 kcal/mol
Surface area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.094, 115.094, 300.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein DeoR-family transcriptional regulator


Mass: 38037.203 Da / Num. of mol.: 2
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
#2: DNA chain DNA (5'-D(P*GP*TP*C)-3')


Mass: 877.623 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*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3')


Mass: 6437.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 1.5 M ammonium sulphate, 0.1 M Tris pH 7.5

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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 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.46→47.3 Å / Num. obs: 14675 / % possible obs: 92.5 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.038 / Net I/σ(I): 9.3
Reflection shellResolution: 3.46→3.56 Å / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1434 / CC1/2: 0.716 / Rpim(I) all: 0.408

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.46→47.3 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3027 1469 10.01 %
Rwork0.2591 --
obs0.2634 14675 90.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.46→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 939 0 0 5793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046038
X-RAY DIFFRACTIONf_angle_d0.8258378
X-RAY DIFFRACTIONf_dihedral_angle_d22.5671161
X-RAY DIFFRACTIONf_chiral_restr0.046936
X-RAY DIFFRACTIONf_plane_restr0.006942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.46-3.580.43381440.36751290X-RAY DIFFRACTION92
3.58-3.730.43081460.33911309X-RAY DIFFRACTION93
3.73-3.90.38251460.33061321X-RAY DIFFRACTION94
3.9-4.10.34331450.31511303X-RAY DIFFRACTION91
4.1-4.360.28531450.29211310X-RAY DIFFRACTION92
4.36-4.690.3241470.28511323X-RAY DIFFRACTION93
4.7-5.170.31391460.27381305X-RAY DIFFRACTION90
5.17-5.910.30561470.27811327X-RAY DIFFRACTION91
5.91-7.440.29481490.24581335X-RAY DIFFRACTION89
7.45-47.30.25071540.19581383X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: -27.9079 Å / Origin y: 19.3161 Å / Origin z: -15.083 Å
111213212223313233
T1.9944 Å20.007 Å2-0.3421 Å2-0.8049 Å20.1355 Å2--1.1517 Å2
L3.6559 °20.5647 °2-0.6651 °2-0.5626 °2-0.0991 °2--1.7776 °2
S-0.9803 Å °0.3176 Å °0.5038 Å °-0.2642 Å °0.504 Å °0.0343 Å °0.0943 Å °0.2516 Å °0.4349 Å °
Refinement TLS groupSelection details: all

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