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- PDB-6a2r: Mycobacterium tuberculosis LexA C-domain II -

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Basic information

Entry
Database: PDB / ID: 6a2r
TitleMycobacterium tuberculosis LexA C-domain II
ComponentsLexA repressor
KeywordsHYDROLASE / Mycobacterium tuberculosis / LexA / SOS response
Function / homology
Function and homology information


repressor LexA / SOS response / DNA-binding transcription repressor activity / peptidoglycan-based cell wall / protein-DNA complex / sequence-specific DNA binding / DNA replication / serine-type endopeptidase activity / response to antibiotic / DNA repair ...repressor LexA / SOS response / DNA-binding transcription repressor activity / peptidoglycan-based cell wall / protein-DNA complex / sequence-specific DNA binding / DNA replication / serine-type endopeptidase activity / response to antibiotic / 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 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 / MOLECULAR REPLACEMENT / Resolution: 2.25 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4128
Polymers71,2006
Non-polymers2122
Water4,288238
1
A: LexA repressor
B: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8393
Polymers23,7332
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LexA repressor
D: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8393
Polymers23,7332
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: LexA repressor
F: LexA repressor


Theoretical massNumber of molelcules
Total (without water)23,7332
Polymers23,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.830, 74.830, 116.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A137 - 236
2111B137 - 236
3111C137 - 236
4111D137 - 236
5111E137 - 236
6111F137 - 236

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.488463, -0.872581, 0.002655), (-0.871818, 0.488159, 0.040417), (-0.036564, 0.017427, -0.999179)37.07896, 20.35428, 77.63329
3given(0.427875, 0.903548, 0.02289), (-0.902508, 0.428482, -0.043384), (-0.049008, -0.002095, 0.998796)-1.14836, 45.06108, -10.30692
4given(0.545508, -0.838102, -0.002422), (-0.838073, -0.54551, 0.007224), (-0.007375, -0.001911, -0.999971)-0.0354, 42.55035, 88.7055
5given(0.792365, -0.609465, -0.026651), (0.605314, 0.790898, -0.089865), (0.075848, 0.055074, 0.995597)42.86791, 53.48342, -12.17229
6given(-0.922139, -0.385654, 0.030499), (-0.386332, 0.922129, -0.020624), (-0.02017, -0.030801, -0.999322)-27.40369, 10.54084, 92.1995

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Components

#1: Protein
LexA repressor


Mass: 11866.654 Da / Num. of mol.: 6 / Fragment: LexA C-domain II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lexA, Rv2720, MTCY05A6.41 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P9WHR7, repressor LexA
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 8.5
Details: 100mM Tris-Hcl, 200mM megnesium chloride, 5% glycerol, 25%PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54179 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.525
11-h,-k,l20.475
ReflectionResolution: 2.25→43.22 Å / Num. obs: 34497 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.09 / Net I/σ(I): 8.9
Reflection shellResolution: 2.25→2.37 Å / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 5017 / CC1/2: 0.462 / Rpim(I) all: 0.401 / % possible all: 100

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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: 2.25→37.41 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / SU B: 3.298 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23822 1653 4.8 %RANDOM
Rwork0.21832 ---
obs0.21932 32811 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: 25.912 Å2
Baniso -1Baniso -2Baniso -3
1-6.2 Å20 Å20 Å2
2--6.2 Å20 Å2
3----12.4 Å2
Refinement stepCycle: 1 / Resolution: 2.25→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 14 238 4728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0154571
X-RAY DIFFRACTIONr_bond_other_d0.0040.0174367
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.7556216
X-RAY DIFFRACTIONr_angle_other_deg0.6411.72210163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.40519.844128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73515627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4481522
X-RAY DIFFRACTIONr_chiral_restr0.0580.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215093
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02779
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_it2.5212.5482373
X-RAY DIFFRACTIONr_mcbond_other2.5212.5482374
X-RAY DIFFRACTIONr_mcangle_it3.6093.8112956
X-RAY DIFFRACTIONr_mcangle_other3.6093.8112957
X-RAY DIFFRACTIONr_scbond_it2.6212.7742198
X-RAY DIFFRACTIONr_scbond_other2.6212.7742198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8224.0793261
X-RAY DIFFRACTIONr_long_range_B_refined5.89931.4174621
X-RAY DIFFRACTIONr_long_range_B_other5.89931.424622
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: 1411 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A5.05
B7.16
C5.46
D4.59
E6.6
F5.83
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 98 -
Rwork0.333 2420 -
obs--99.96 %

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