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- PDB-3k2z: Crystal structure of a LexA protein from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3k2z
TitleCrystal structure of a LexA protein from Thermotoga maritima
ComponentsLexA repressor
KeywordsHYDROLASE / winged helix-turn-helix / repressor / LexA / SOS system / Autocatalytic cleavage / DNA damage / DNA repair / DNA replication / DNA-binding / SOS response / Transcription / Transcription regulation
Function / homology
Function and homology information


repressor LexA / SOS response / DNA replication / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA binding
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
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.37 Å
AuthorsZhang, A.P.P. / Rice, P.A.
CitationJournal: To be Published
Title: Crystal structure of a LexA protein from Thermotoga maritima
Authors: Zhang, A.P.P. / Rice, P.A.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LexA repressor
B: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5273
Polymers45,4352
Non-polymers921
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-7 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.770, 62.676, 57.017
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LexA repressor


Mass: 22717.490 Da / Num. of mol.: 2 / Mutation: K156A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: lexA, TM_1082 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: O33927, repressor LexA
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 292 K / Method: hanging drop / pH: 6.8
Details: 0.1M Bis-tris propane, 0.4M ammonium sulfate, 10% glycerol, pH 6.8, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2005 / Details: mirros
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.37→25 Å / Num. all: 85313 / Num. obs: 85313 / Redundancy: 3.6 % / Rsym value: 0.044 / Net I/σ(I): 21.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MLPHAREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.37→13.51 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.012 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 6440 8.1 %RANDOM
Rwork0.203 ---
obs0.205 79525 92.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.14 Å2 / Biso mean: 18.569 Å2 / Biso min: 5.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.37→13.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 6 378 3541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223226
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9874322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.84722.372156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28415636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5551540
X-RAY DIFFRACTIONr_chiral_restr0.0850.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022401
X-RAY DIFFRACTIONr_nbd_refined0.190.21311
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.227
X-RAY DIFFRACTIONr_mcbond_it1.2871.52005
X-RAY DIFFRACTIONr_mcangle_it1.89723109
X-RAY DIFFRACTIONr_scbond_it3.74131372
X-RAY DIFFRACTIONr_scangle_it4.0434.51213
X-RAY DIFFRACTIONr_rigid_bond_restr3.57433377
X-RAY DIFFRACTIONr_sphericity_free4.6093378
X-RAY DIFFRACTIONr_sphericity_bonded3.81633174
LS refinement shellResolution: 1.37→1.402 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 393 -
Rwork0.223 4487 -
all-4880 -
obs--78.16 %

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