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- PDB-1jhe: LEXA L89P Q92W E152A K156A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1jhe
TitleLEXA L89P Q92W E152A K156A MUTANT
ComponentsLEXA REPRESSOR
KeywordsHYDROLASE / LexA SOS repressor / C-terminal
Function / homology
Function and homology information


repressor LexA / SOS response / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / DNA replication / transcription cis-regulatory region binding / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription ...repressor LexA / SOS response / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / 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 / Umud Fragment, subunit A / Umud Fragment, subunit A / : / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like ...LexA repressor, DNA-binding domain / Transcription regulator LexA / LexA DNA binding domain / Peptidase S24, LexA-like / Umud Fragment, subunit A / Umud Fragment, subunit A / : / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Ribbon / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, Y. / Pfuetzner, R.A. / Mosimann, S. / Little, J.W. / J Strynadka, N.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Crystal structure of LexA: a conformational switch for regulation of self-cleavage.
Authors: Luo, Y. / Pfuetzner, R.A. / Mosimann, S. / Paetzel, M. / Frey, E.A. / Cherney, M. / Kim, B. / Little, J.W. / Strynadka, N.C.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEXA REPRESSOR
B: LEXA REPRESSOR


Theoretical massNumber of molelcules
Total (without water)29,8482
Polymers29,8482
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.700, 43.700, 49.500
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LEXA REPRESSOR


Mass: 14924.055 Da / Num. of mol.: 2 / Fragment: C-Terminus, Residues 68-202 / Mutation: L89P,Q92W,E152A,K156A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LexA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7C2, repressor LexA
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 1500, 0.1 M MES buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG15001reservoir
20.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 20, 2000 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 9700 / Num. obs: 9700 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.3 / Num. unique all: 486 / Rsym value: 0.431 / % possible all: 95.1
Reflection
*PLUS
Num. obs: 8960 / Num. measured all: 30913
Reflection shell
*PLUS
% possible obs: 95.1 % / Num. unique obs: 486

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JHC

1jhc


Resolution: 2.5→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 819 -RANDOM
Rwork0.22 ---
all-7992 --
obs-7992 90.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 0 17 1925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.52
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.22 / Rfactor Rwork: 0.22 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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