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- PDB-7tzv: Structure of DriD C-domain bound to 9mer ssDNA -

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Basic information

Entry
Database: PDB / ID: 7tzv
TitleStructure of DriD C-domain bound to 9mer ssDNA
Components
  • DNA (5'-D(*TP*AP*GP*TP*CP*TP*AP*CP*T)-3')
  • WYL domain-containing protein
KeywordsTRANSCRIPTION / DriD / DNA repair / SOS-independent / WYL domain / wHTH
Function / homologyProtein PafC / WCX domain / : / WYL domain profile. / WYL domain / WYL domain / DNA / WYL domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSchumacher, M.A. / Laub, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Genes Dev. / Year: 2022
Title: ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD.
Authors: Gozzi, K. / Salinas, R. / Nguyen, V.D. / Laub, M.T. / Schumacher, M.A.
History
DepositionFeb 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WYL domain-containing protein
M: WYL domain-containing protein
J: DNA (5'-D(*TP*AP*GP*TP*CP*TP*AP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)46,7723
Polymers46,7723
Non-polymers00
Water8,035446
1
A: WYL domain-containing protein
M: WYL domain-containing protein

J: DNA (5'-D(*TP*AP*GP*TP*CP*TP*AP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)46,7723
Polymers46,7723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area7050 Å2
ΔGint-35 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.023, 85.338, 93.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein WYL domain-containing protein


Mass: 22032.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A999
#2: DNA chain DNA (5'-D(*TP*AP*GP*TP*CP*TP*AP*CP*T)-3')


Mass: 2705.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 0.1 M Imidazole, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.01 Å
DetectorType: DECTRIS EIGER2 S 4M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 1.65→36.1 Å / Num. obs: 55422 / % possible obs: 98.1 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rsym value: 0.049 / Net I/σ(I): 16.1
Reflection shellResolution: 1.65→1.69 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3432 / CC1/2: 0.886 / Rpim(I) all: 0.978 / Rsym value: 1.245

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DriD Cdomain, p3121 form

Resolution: 1.65→31.49 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1998 3.61 %
Rwork0.1917 53424 -
obs0.1929 55422 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.17 Å2 / Biso mean: 37.8593 Å2 / Biso min: 17.1 Å2
Refinement stepCycle: final / Resolution: 1.65→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 179 0 446 3640
Biso mean---47.86 -
Num. residues----394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.690.30471200.2953216333683
1.69-1.740.30181320.25343532366492
1.74-1.790.30741430.237738243967100
1.79-1.850.25221440.236838433987100
1.85-1.910.29561430.26738243967100
1.91-1.990.29231440.243538744018100
1.99-2.080.27521440.212538483992100
2.08-2.190.25491440.206638383982100
2.19-2.330.25461450.22183871401699
2.33-2.50.23731460.209638814027100
2.5-2.760.23141460.209139004046100
2.76-3.160.21591450.198639094054100
3.16-3.970.23641480.168439564104100
3.97-31.490.15651540.151941084262100
Refinement TLS params.Method: refined / Origin x: -16.0599 Å / Origin y: 2.1979 Å / Origin z: -8.0916 Å
111213212223313233
T0.1666 Å2-0.0091 Å2-0 Å2-0.1704 Å20.0002 Å2--0.2097 Å2
L0.7257 °2-0.3915 °20.1575 °2-1.0186 °2-0.2834 °2--0.9979 °2
S-0.0391 Å °-0.0377 Å °0.2014 Å °0.099 Å °-0.0128 Å °-0.0754 Å °-0.1239 Å °0.0899 Å °0.0519 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allM136 - 327
2X-RAY DIFFRACTION1allA135 - 327
3X-RAY DIFFRACTION1allJ16 - 24
4X-RAY DIFFRACTION1allS1 - 463

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