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- PDB-1jhc: LEXA S119A C-TERMINAL TRYPTIC FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1jhc
TitleLEXA S119A C-TERMINAL TRYPTIC FRAGMENT
ComponentsLEXA REPRESSOR
KeywordsHYDROLASE / LexA SOS repressor
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 Å
AuthorsLuo, Y. / Pfuetzner, R.A. / Mosimann, S. / Little, J.W. / Strynadka, N.C.J.
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

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Assembly

Deposited unit
A: LEXA REPRESSOR


Theoretical massNumber of molelcules
Total (without water)15,1781
Polymers15,1781
Non-polymers00
Water45025
1
A: LEXA REPRESSOR

A: LEXA REPRESSOR


Theoretical massNumber of molelcules
Total (without water)30,3572
Polymers30,3572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)49.880, 49.880, 103.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimer generated by crystallographic symmetry

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Components

#1: Protein LEXA REPRESSOR


Mass: 15178.403 Da / Num. of mol.: 1 / Fragment: C-Terminus, Residues 68-202 / Mutation: S119A
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.: 25 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6 Mpotassium phosphate1reservoir
20.3 MTris-HCl1reservoir

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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: Oct 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→20 Å / Num. all: 10911 / Num. obs: 10911 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 32.5
Reflection shellResolution: 2→2.04 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 6.8 / Num. unique all: 520 / Rsym value: 0.341 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 9882 / Num. measured all: 90223
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 8.5 % / Num. unique obs: 520

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Processing

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

1umu


Resolution: 2→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
Rfree0.278 948 -RANDOM
Rwork0.23 ---
all-9206 --
obs-9206 98.8 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 0 25 1031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.079
X-RAY DIFFRACTIONc_angle_deg1.51
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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