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- PDB-3k3r: Unrefined crystal structure of a LexA-DNA complex -

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Basic information

Entry
Database: PDB / ID: 3k3r
TitleUnrefined crystal structure of a LexA-DNA complex
Components
  • DNA (28-MER)
  • LexA repressor
KeywordsHYDROLASE/DNA / protein-DNA complex / winged helix-turn-helix / double helix / repressor / LexA / SOS system / Autocatalytic cleavage / DNA damage / DNA repair / DNA replication / DNA-binding / Hydrolase / SOS response / Transcription / Transcription regulation / HYDROLASE-DNA COMPLEX
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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / LexA repressor
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsZhang, A.P.P. / Pigli, Y.Z. / Rice, P.A.
CitationJournal: Nature / Year: 2010
Title: Structure of the LexA-DNA complex and implications for SOS box measurement.
Authors: Zhang, A.P. / Pigli, Y.Z. / Rice, P.A.
History
DepositionOct 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: LexA repressor
F: LexA repressor
A: DNA (28-MER)
B: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)62,5254
Polymers62,5254
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.357, 120.393, 149.814
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 LexA repressor / Coordinate model: Cα atoms only


Mass: 22330.611 Da / Num. of mol.: 2 / Mutation: K156A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: lexA, exrA, spr, tsl, umuA, b4043, JW4003 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A7C2, repressor LexA
#2: DNA chain DNA (28-MER) / Coordinate model: P atoms only


Mass: 8931.795 Da / Num. of mol.: 2 / Source method: obtained synthetically

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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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 292 K / Method: hanging drop / pH: 8.5
Details: 40mM Tris-HCl, 1mM EDTA, 10mM MgCl2, 0.1M NaCl, 5mM spermidine, 10% glycerol, 12% (w/v) PEG5000, pH 8.5, hanging drop, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCl11
2EDTA11
3MgCl211
4NaCl11
5spermidine11
6glycerol11
7PEG500011
8Tris-HCl12
9EDTA12
10MgCl212
11NaCl12
12spermidine12
13glycerol12
14PEG500012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 2, 2007 / Details: mirros
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 14447 / Num. obs: 14447 / Redundancy: 5.6 % / Rsym value: 0.123 / Net I/σ(I): 13.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementResolution: 3.2→50 Å / Num. reflection all: 14447 / Num. reflection obs: 14447 / Occupancy max: 1 / Occupancy min: 1
Details: This is an unrefined, Ca/P only, protein/DNA crystal structure
Displacement parametersBiso max: 136.82 Å2 / Biso min: 26.48 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms347 56 0 0 403

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