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- PDB-6a2s: Mycobacterium tuberculosis LexA C-domain S160A -

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Basic information

Entry
Database: PDB / ID: 6a2s
TitleMycobacterium tuberculosis LexA C-domain S160A
ComponentsLexA repressor
KeywordsHYDROLASE / Mycobacterium tuberculosis / LexA / SOS response
Function / homology
Function and homology information


repressor LexA / SOS response / peptidoglycan-based cell wall / DNA replication / response to antibiotic / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / proteolysis / 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 / Ribbon / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / LexA repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChandran, A.V. / Srikalaivani, R. / Paul, A. / Vijayan, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Biochemical characterization of Mycobacterium tuberculosis LexA and structural studies of its C-terminal segment.
Authors: Chandran, A.V. / Srikalaivani, R. / Paul, A. / Vijayan, M.
History
DepositionJun 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: LexA repressor
D: LexA repressor
E: LexA repressor
F: LexA repressor
G: LexA repressor
H: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,21918
Polymers94,8058
Non-polymers1,41410
Water3,117173
1
A: LexA repressor
B: LexA repressor
C: LexA repressor
D: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,60412
Polymers47,4034
Non-polymers1,2018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: LexA repressor
F: LexA repressor
G: LexA repressor
H: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6156
Polymers47,4034
Non-polymers2122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.610, 104.200, 88.100
Angle α, β, γ (deg.)90.00, 104.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A136 - 236
2111B136 - 236
3111C136 - 236
4111D136 - 236
5111E136 - 236
6111F136 - 236
7111G136 - 236
8111H136 - 236

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.50881, -0.860549, -0.023822), (-0.860517, 0.509203, -0.014901), (0.024954, 0.012917, -0.999605)29.82794, 16.88748, 127.65394
3given(-0.999999, 0.001159, -0.001117), (-0.00112, -0.999401, -0.034588), (-0.001156, -0.034586, 0.999401)-5.51061, 72.17635, 1.04486
4given(0.500116, 0.865249, 0.035032), (0.865916, -0.499283, -0.030091), (-0.008545, 0.045384, -0.998933)-31.40046, 58.04866, 126.75109
5given(0.229051, 0.470306, 0.852261), (-0.440429, -0.73072, 0.521604), (0.868077, -0.494834, 0.039764)-37.64172, 54.92718, 72.21117
6given(0.266591, 0.393152, -0.879977), (-0.433551, -0.766513, -0.473805), (-0.860792, 0.507828, -0.033894)0.10468, 76.27955, 55.43289
7given(-0.223388, -0.499576, -0.836972), (0.517352, 0.666971, -0.536187), (0.826102, -0.552787, 0.109464)37.76958, 18.91826, 73.86979
8given(-0.266745, -0.390801, 0.880978), (0.433713, 0.767632, 0.471841), (-0.860663, 0.507953, -0.035266)-5.20144, -6.71671, 55.39576

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Components

#1: Protein
LexA repressor


Mass: 11850.654 Da / Num. of mol.: 8 / Fragment: LexA C-domain / Mutation: S160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: lexA, Rv2720, MTCY05A6.41 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Plysis / References: UniProt: P9WHR7, repressor LexA
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: 100mM Bis-Tris, 200mM megnesium chloride, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→66.16 Å / Num. obs: 35018 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.053 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 1.119 / Num. unique obs: 5104 / CC1/2: 0.754 / Rpim(I) all: 0.437

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IUMU

Resolution: 2.5→66.16 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.883 / SU B: 15.421 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29003 1709 4.9 %RANDOM
Rwork0.24147 ---
obs0.24389 33284 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.426 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å21.7 Å2
2---3.85 Å20 Å2
3---4.3 Å2
Refinement stepCycle: 1 / Resolution: 2.5→66.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5778 0 94 173 6045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0156045
X-RAY DIFFRACTIONr_bond_other_d0.010.0175760
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.7738190
X-RAY DIFFRACTIONr_angle_other_deg0.8451.76613348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5319.481154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16415766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4981527
X-RAY DIFFRACTIONr_chiral_restr0.0610.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216697
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021031
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5646.3033192
X-RAY DIFFRACTIONr_mcbond_other4.5646.3033193
X-RAY DIFFRACTIONr_mcangle_it7.4229.4383976
X-RAY DIFFRACTIONr_mcangle_other7.4229.4383977
X-RAY DIFFRACTIONr_scbond_it3.9296.2122853
X-RAY DIFFRACTIONr_scbond_other3.9286.2122853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1989.1894215
X-RAY DIFFRACTIONr_long_range_B_refined10.24874.5665998
X-RAY DIFFRACTIONr_long_range_B_other10.24774.5625998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1212 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A21.96
B14.62
C22.17
D13.07
E8.2
F17.21
G19.58
H14.58
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 117 -
Rwork0.338 2449 -
obs--100 %

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