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- PDB-6yj2: Structural and DNA binding studies of the transcriptional repress... -

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Basic information

Entry
Database: PDB / ID: 6yj2
TitleStructural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism
ComponentsProbable transcriptional regulatory protein (Probably TetR-family)
KeywordsDNA BINDING PROTEIN / Tuberculosis / Branch-chain amino acid catabolism / TetR Family
Function / homology
Function and homology information


evasion of host immune response / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Probable transcriptional regulatory protein (Probably TetR-family)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKeep, N.H. / Pritchard, J.E. / Sula, A. / Cole, A.R. / Kendall, S.L.
CitationJournal: To be published
Title: Structural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism
Authors: Pritchard, J.E. / Sula, A. / Cole, A.R. / Kendall, S.L. / Keep, N.H.
History
DepositionApr 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable transcriptional regulatory protein (Probably TetR-family)
D: Probable transcriptional regulatory protein (Probably TetR-family)
A: Probable transcriptional regulatory protein (Probably TetR-family)
C: Probable transcriptional regulatory protein (Probably TetR-family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,75212
Polymers93,0154
Non-polymers7378
Water4,396244
1
B: Probable transcriptional regulatory protein (Probably TetR-family)
A: Probable transcriptional regulatory protein (Probably TetR-family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8766
Polymers46,5072
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-30 kcal/mol
Surface area17670 Å2
MethodPISA
2
D: Probable transcriptional regulatory protein (Probably TetR-family)
C: Probable transcriptional regulatory protein (Probably TetR-family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8766
Polymers46,5072
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-25 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.764, 52.874, 91.919
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12B
22A
13B
23C
14D
24A
15D
25C
16A
26C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUBA24 - 21524 - 215
21SERSERLEULEUDB24 - 21524 - 215
12ASPASPCYSCYSBA25 - 21425 - 214
22ASPASPCYSCYSAC25 - 21425 - 214
13PHEPHECYSCYSBA28 - 21428 - 214
23PHEPHECYSCYSCD28 - 21428 - 214
14ASPASPCYSCYSDB25 - 21425 - 214
24ASPASPCYSCYSAC25 - 21425 - 214
15PHEPHECYSCYSDB28 - 21428 - 214
25PHEPHECYSCYSCD28 - 21428 - 214
16PHEPHEARGARGAC28 - 21328 - 213
26PHEPHEARGARGCD28 - 21328 - 213

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Probable transcriptional regulatory protein (Probably TetR-family)


Mass: 23253.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv2506 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06169
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.22 M ammonium citrate tribasic pH 7.0, 26.4 % (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→46 Å / Num. obs: 59229 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.034 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4355 / CC1/2: 0.808 / Rpim(I) all: 0.351 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G12

4g12


Resolution: 2→46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.343 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.15
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 2946 5 %RANDOM
Rwork0.192 ---
obs0.1936 56283 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 189.62 Å2 / Biso mean: 51.997 Å2 / Biso min: 21.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å2-0 Å2-0.14 Å2
2---2.19 Å20 Å2
3---1.67 Å2
Refinement stepCycle: final / Resolution: 2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5752 0 48 244 6044
Biso mean--61.09 49 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175828
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6317936
X-RAY DIFFRACTIONr_angle_other_deg1.3391.57513295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.86418.805343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48815970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1811581
X-RAY DIFFRACTIONr_chiral_restr0.0760.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021366
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B58070.09
12D58070.09
21B56690.09
22A56690.09
31B54590.1
32C54590.1
41D56060.1
42A56060.1
51D55210.09
52C55210.09
61A54590.09
62C54590.09
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 221 -
Rwork0.277 4123 -
all-4344 -
obs--99.68 %

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