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- PDB-3jso: Classic Protein With a New Twist: crystal structure of a LexA rep... -

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Basic information

Entry
Database: PDB / ID: 3jso
TitleClassic Protein With a New Twist: crystal structure of a LexA repressor DNA complex
Components
  • DNA (5'-D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*A)-3')
  • LexA repressorRepressor lexA
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 / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily ...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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Ribbon / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / LexA repressor
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, molecular replacement / MAD / molecular replacement / Resolution: 2.29 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
DepositionSep 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: 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
A: LexA repressor
B: LexA repressor
C: DNA (5'-D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*A)-3')
D: DNA (5'-D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)58,1584
Polymers58,1584
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-49 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.975, 106.935, 65.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a dimeric protein (chains A & B) bound to a DNA duplex (chains C & D).

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Components

#1: Protein LexA repressor / Repressor lexA


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 (5'-D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*A)-3')


Mass: 6748.415 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 292 K / Method: hanging drop / pH: 6.8
Details: 0.1M Bis-tris propane, 0.05M sodium tartrate, 10% glycerol, 15% ethylene glycol, 14% (w/v) PEG3350, pH 6.8, hanging drop, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis-tris propane11
2sodium tartrate11
3glycerol11
4ethylene glycol11
5PEG335011
6Bis-tris propane12
7sodium tartrate12
8glycerol12
9ethylene glycol12
10PEG335012

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2008 / Details: mirros
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 23570 / Num. obs: 23570 / % possible obs: 72.2 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 5.4 % / Rsym value: 0.065 / Net I/σ(I): 21.4

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVEphasing
DMphasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD, molecular replacement / Resolution: 2.29→37.53 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.892 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 37.021 / SU ML: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.634 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1084 5 %RANDOM
Rwork0.266 ---
obs0.268 21609 66.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.3 Å2 / Biso mean: 84.018 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.36 Å2-0 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.29→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 896 0 81 3879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223963
X-RAY DIFFRACTIONr_angle_refined_deg0.9152.2655535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8265375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85523.657134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31415544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.961531
X-RAY DIFFRACTIONr_chiral_restr0.0480.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212671
X-RAY DIFFRACTIONr_mcbond_it0.0991.51876
X-RAY DIFFRACTIONr_mcangle_it0.17923017
X-RAY DIFFRACTIONr_scbond_it0.28332087
X-RAY DIFFRACTIONr_scangle_it0.5274.52518
LS refinement shellResolution: 2.29→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 24 -
Rwork0.519 320 -
all-344 -
obs--14.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6295-0.1189-0.72135.6193-3.875510.45730.1630.4672-0.3655-1.0690.16120.82451.2507-1.0383-0.32430.4055-0.1056-0.15130.4189-0.07610.266412.9327.383-11.27
23.3563-0.89363.134.7749-2.997410.3672-0.031-0.5224-0.13330.95160.45360.84060.2048-1.2905-0.42270.4256-0.07990.17730.39160.02140.258114.2364.15623.39
35.30060.1344-0.9617.9905-0.41310.1320.13650.31180.0446-0.4894-0.1855-0.47170.18750.45430.04910.2046-0.08660.03380.225-0.0210.084225.90413.315-6.311
44.59820.98612.10467.5846-1.073510.3114-0.0450.0880.09020.9475-0.0541-0.52280.37080.49330.0990.2073-0.0054-0.04060.3259-0.03920.136827.7059.13318.32
52.46860.5064-1.60565.489-4.259510.5237-0.1387-0.0023-0.0844-0.07380.1240.31820.7151-0.56240.01460.4055-0.05090.00640.3078-0.0930.266767.62216.1659.515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 12
2X-RAY DIFFRACTION1D13 - 22
3X-RAY DIFFRACTION2C13 - 22
4X-RAY DIFFRACTION2D1 - 12
5X-RAY DIFFRACTION3A2 - 69
6X-RAY DIFFRACTION4B2 - 69
7X-RAY DIFFRACTION5A76 - 198
8X-RAY DIFFRACTION5B76 - 198

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