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- PDB-6yl2: Structural and DNA binding studies of the transcriptional repress... -

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Basic information

Entry
Database: PDB / ID: 6yl2
TitleStructural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism
Components
  • DNA (5'-D(*AP*CP*GP*TP*TP*AP*AP*TP*GP*AP*CP*GP*AP*TP*TP*AP*AP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*TP*TP*AP*AP*TP*CP*GP*TP*CP*AP*TP*TP*AP*AP*CP*GP*T)-3')
  • Probable 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
DNA / DNA (> 10) / Probable transcriptional regulatory protein (Probably TetR-family)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 6, 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)
A: Probable transcriptional regulatory protein (Probably TetR-family)
G: DNA (5'-D(*AP*CP*GP*TP*TP*AP*AP*TP*GP*AP*CP*GP*AP*TP*TP*AP*AP*CP*CP*G)-3')
H: DNA (5'-D(*CP*GP*GP*TP*TP*AP*AP*TP*CP*GP*TP*CP*AP*TP*TP*AP*AP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)54,7794
Polymers54,7794
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-65 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.409, 66.000, 179.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 24 - 215 / Label seq-ID: 5 - 196

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

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


Mass: 21256.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv2506 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O06169
#2: DNA chain DNA (5'-D(*AP*CP*GP*TP*TP*AP*AP*TP*GP*AP*CP*GP*AP*TP*TP*AP*AP*CP*CP*G)-3')


Mass: 6142.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
#3: DNA chain DNA (5'-D(*CP*GP*GP*TP*TP*AP*AP*TP*CP*GP*TP*CP*AP*TP*TP*AP*AP*CP*GP*T)-3')


Mass: 6123.977 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)

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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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium citrate pH 5.5, 5% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 3.15→62.03 Å / Num. obs: 12331 / % possible obs: 98.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 74.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.02 / Net I/σ(I): 11.7
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 597 / CC1/2: 0.982 / Rpim(I) all: 0.181 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YJ2

6yj2


Resolution: 3.15→62.03 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.953 / SU B: 115.719 / SU ML: 0.701 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 618 5 %RANDOM
Rwork0.2671 ---
obs0.2679 11698 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 245.34 Å2 / Biso mean: 147.485 Å2 / Biso min: 105.52 Å2
Baniso -1Baniso -2Baniso -3
1-18.8 Å20 Å20 Å2
2---2.28 Å2-0 Å2
3----16.52 Å2
Refinement stepCycle: final / Resolution: 3.15→62.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 814 0 0 3740
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0143928
X-RAY DIFFRACTIONr_bond_other_d0.0080.0173386
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.5145422
X-RAY DIFFRACTIONr_angle_other_deg1.4791.7737766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.195.331592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.22218.75176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06815494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2511542
X-RAY DIFFRACTIONr_chiral_restr0.2110.222542
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023888
X-RAY DIFFRACTIONr_gen_planes_other0.0280.02890
Refine LS restraints NCS

Ens-ID: 1 / Number: 5844 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 3.15→3.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 45 -
Rwork0.485 842 -
all-887 -
obs--99.33 %
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)
10.8701-0.43641.13020.90390.67035.88810.09090.1408-0.1582-0.266-0.0099-0.3587-0.03260.1954-0.0811.2135-0.0770.02891.13330.11781.29711.907232.074724.2239
20.6337-0.1554-0.93380.9755-0.90845.19720.04020.19270.1092-0.251-0.03040.1710.18720.1298-0.00971.2790.0016-0.021.2096-0.07131.388517.723410.581924.1405
32.538-1.1513-0.4396.0961-0.97062.8398-0.1682-0.532-0.10621.4138-0.2709-0.63110.041-0.22020.4391.2388-0.0557-0.13090.32370.00781.284614.85421.317657.8979
41.5078-0.9624-0.0465.6943-0.32530.8546-0.0292-0.4273-0.05410.5201-0.1815-0.198-0.0130.22760.21071.4135-0.0402-0.01750.4286-0.01781.263914.074121.313357.924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B24 - 215
2X-RAY DIFFRACTION2A24 - 215
3X-RAY DIFFRACTION3G1 - 20
4X-RAY DIFFRACTION4H1 - 20

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