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- PDB-7b5g: Crystal structure of E.coli LexA in complex with nanobody NbSOS3(... -

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Basic information

Entry
Database: PDB / ID: 7b5g
TitleCrystal structure of E.coli LexA in complex with nanobody NbSOS3(Nb14527)
Components
  • LexA repressor
  • Nanobody Nb14527, NbSOS3
KeywordsTRANSCRIPTION / Transcriptional repressor DNA binding autoproteolysis Nanobodies
Function / homology
Function and homology information


repressor LexA / SOS response / DNA-binding transcription repressor activity / protein-DNA complex / DNA replication / transcription cis-regulatory region binding / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription ...repressor LexA / SOS response / DNA-binding transcription repressor activity / protein-DNA complex / DNA replication / transcription cis-regulatory region binding / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA damage response / proteolysis / DNA binding / identical protein binding / cytosol
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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
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 1.2Nov 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 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
A: LexA repressor
B: Nanobody Nb14527, NbSOS3
C: LexA repressor
D: Nanobody Nb14527, NbSOS3
E: LexA repressor
F: Nanobody Nb14527, NbSOS3
G: LexA repressor
H: Nanobody Nb14527, NbSOS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,12514
Polymers146,7538
Non-polymers3726
Water2,126118
1
A: LexA repressor
B: Nanobody Nb14527, NbSOS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8124
Polymers36,6882
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LexA repressor
D: Nanobody Nb14527, NbSOS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9376
Polymers36,6882
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: LexA repressor
F: Nanobody Nb14527, NbSOS3


Theoretical massNumber of molelcules
Total (without water)36,6882
Polymers36,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: LexA repressor
H: Nanobody Nb14527, NbSOS3


Theoretical massNumber of molelcules
Total (without water)36,6882
Polymers36,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.067, 57.081, 122.506
Angle α, β, γ (deg.)84.530, 83.210, 68.430
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
LexA repressor


Mass: 22388.713 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: First 70 residues are not visible in the electron density maps.
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lexA, exrA, spr, tsl, umuA, b4043, JW4003 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A7C2, repressor LexA
#2: Antibody
Nanobody Nb14527, NbSOS3


Mass: 14299.536 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-term and fusion tag are not visible in the electron density maps
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.15 M sodium chloride, 0.05 M HEPES, 24 % w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 2.4→53.06 Å / Num. obs: 47061 / % possible obs: 98.2 % / Redundancy: 2.4 % / CC1/2: 0.923 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1 / Num. unique obs: 4685

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JHF

1jhf


Resolution: 2.4→49.61 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.252 --RANDOM
Rwork0.206 ---
obs-46989 98.04 %-
Displacement parametersBiso max: 130.69 Å2 / Biso mean: 46.1177 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7789 0 24 118 7931

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