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- PDB-9cu3: Allosteric mechanism of DriD transcription activator -

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Basic information

Entry
Database: PDB / ID: 9cu3
TitleAllosteric mechanism of DriD transcription activator
ComponentsWYL domain-containing protein
KeywordsDNA BINDING PROTEIN / Transcription / activation
Function / homologyProtein PafC / WCX domain / : / WYL domain profile. / WYL domain / WYL domain / WYL domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCannistraci, E.G. / Schumacher, 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: Commun Biol / Year: 2025
Title: Allosteric activation mechanism of DriD, a WYL-domain containing transcription regulator.
Authors: Cannistraci, E. / Srinivasu, B.Y. / Chavez Orozco Jr., J. / Gozzi, K. / Wales, T.E. / Schumacher, M.A.
History
DepositionJul 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: WYL domain-containing protein
A: WYL domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9528
Polymers59,3832
Non-polymers5686
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-111 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.796, 88.796, 141.523
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein WYL domain-containing protein


Mass: 29691.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides CB15 (bacteria) / Gene: CC_1095 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A999
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ammonium sulfate dibasic, sodium cacodylate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.02 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.9→46.73 Å / Num. obs: 46532 / % possible obs: 95.1 % / Redundancy: 7.9 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.032 / Rrim(I) all: 0.092 / Net I/σ(I): 10.4
Reflection shellResolution: 2.19→2.31 Å / % possible obs: 73.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.574 / Num. measured all: 12020 / Num. unique obs: 3557 / CC1/2: 0.911 / Rpim(I) all: 0.347 / Rrim(I) all: 0.676 / Net I/σ(I) obs: -0.4

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Processing

Software
NameVersionClassification
PHENIX1.21-5207refinement
Aimless8.0.012data scaling
XDS8.0.012data reduction
PHASER1.21-5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.4 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 1966 4.23 %
Rwork0.2021 --
obs0.2033 46531 90.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 32 552 3709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075
X-RAY DIFFRACTIONf_angle_d0.845
X-RAY DIFFRACTIONf_dihedral_angle_d17.2081186
X-RAY DIFFRACTIONf_chiral_restr0.049463
X-RAY DIFFRACTIONf_plane_restr0.008575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.7906730.77741624X-RAY DIFFRACTION47
1.95-20.52251060.4562500X-RAY DIFFRACTION72
2-2.060.30561420.27163165X-RAY DIFFRACTION91
2.06-2.130.22931500.22843404X-RAY DIFFRACTION98
2.13-2.20.25261530.21323480X-RAY DIFFRACTION100
2.2-2.290.4953920.43292113X-RAY DIFFRACTION61
2.29-2.390.28841500.22613412X-RAY DIFFRACTION97
2.39-2.520.24071550.21063504X-RAY DIFFRACTION100
2.52-2.680.2271570.19863490X-RAY DIFFRACTION100
2.68-2.880.21811520.20213524X-RAY DIFFRACTION100
2.89-3.170.25771550.19223543X-RAY DIFFRACTION100
3.18-3.630.20971550.15463531X-RAY DIFFRACTION100
3.63-4.580.17691570.1483547X-RAY DIFFRACTION99
4.58-100.16361690.15913728X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 42.2629 Å / Origin y: -33.2382 Å / Origin z: -11.1163 Å
111213212223313233
T0.1734 Å20.0865 Å20.0082 Å2-0.435 Å20.0359 Å2--0.2953 Å2
L1.4175 °2-0.1543 °20.6798 °2-0.3919 °2-0.166 °2--1.6619 °2
S-0.1052 Å °-0.0245 Å °0.1351 Å °0.1272 Å °0.094 Å °0.0257 Å °-0.1997 Å °-0.2439 Å °0.0079 Å °
Refinement TLS groupSelection details: all

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