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- PDB-7ocj: Crystal structure of E.coli LexA in complex with nanobody NbSOS2(... -

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Basic information

Entry
Database: PDB / ID: 7ocj
TitleCrystal structure of E.coli LexA in complex with nanobody NbSOS2(Nb14509)
Components
  • LexA repressor
  • NbSOS2 (14509)
KeywordsTRANSCRIPTION / Transcriptional repressor DNA binding autoproteolysis Nanobodies
Function / homology
Function and homology information


repressor LexA / SOS response / DNA replication / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / proteolysis / DNA binding
Similarity search - Function
LexA repressor, DNA-binding domain / Transcription regulator LexA / LexA DNA binding domain / Peptidase S24, LexA-like / : / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMaso, L. / Vascon, F. / Chinellato, M. / Pardon, E. / Steyaert, J. / Angelini, A. / Tondi, D. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Structure / Year: 2022
Title: Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway.
Authors: Maso, L. / Vascon, F. / Chinellato, M. / Goormaghtigh, F. / Bellio, P. / Campagnaro, E. / Van Melderen, L. / Ruzzene, M. / Pardon, E. / Angelini, A. / Celenza, G. / Steyaert, J. / Tondi, D. / Cendron, L.
History
DepositionApr 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
G: NbSOS2 (14509)
A: LexA repressor
C: LexA repressor
E: NbSOS2 (14509)
B: NbSOS2 (14509)
D: LexA repressor
F: LexA repressor
H: NbSOS2 (14509)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,9949
Polymers147,9328
Non-polymers621
Water82946
1
G: NbSOS2 (14509)
A: LexA repressor
C: LexA repressor
E: NbSOS2 (14509)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0285
Polymers73,9664
Non-polymers621
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-22 kcal/mol
Surface area22230 Å2
MethodPISA
2
B: NbSOS2 (14509)
D: LexA repressor
F: LexA repressor
H: NbSOS2 (14509)


Theoretical massNumber of molelcules
Total (without water)73,9664
Polymers73,9664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-22 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.672, 112.672, 144.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody
NbSOS2 (14509)


Mass: 12422.886 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein
LexA repressor


Mass: 24560.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: missing residues are not visible in the electron density maps
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lexA, EAMG_02325 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3HXW2, repressor LexA
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5, 30 % w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.7→48.79 Å / Num. obs: 28568 / % possible obs: 96.2 % / Redundancy: 7.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8056 / CC1/2: 0.558

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JHF

1jhf


Resolution: 2.7→48.25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.26 --
Rwork0.228 --
obs-28566 96.08 %
Displacement parametersBiso max: 93.72 Å2 / Biso mean: 47.6129 Å2 / Biso min: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7520 0 4 46 7570

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