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- PDB-8ioi: Crystal Structure of PadR- family transcriptional regulator Rv117... -

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Basic information

Entry
Database: PDB / ID: 8ioi
TitleCrystal Structure of PadR- family transcriptional regulator Rv1176c from Mycobacterium tuberculosis H37Rv.
ComponentsPadR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Transcriptional regulator
Function / homologyTranscription regulator PadR, C-terminal / Virulence activator alpha C-term / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / peptidoglycan-based cell wall / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / PadR family transcriptional regulator
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsYadav, V. / Zohib, M. / Pal, R.K. / Biswal, B.K. / Arora, A.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2021/007117 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural and biophysical characterization of PadR family protein Rv1176c of Mycobacterium tuberculosis H37Rv.
Authors: Yadav, V. / Zohib, M. / Singh, S. / Pal, R.K. / Tripathi, S. / Jain, A. / Biswal, B.K. / Dasgupta, A. / Arora, A.
History
DepositionMar 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PadR family transcriptional regulator
B: PadR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3385
Polymers42,9282
Non-polymers4103
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size Exclusion Chromatography was done
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-26 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.446, 119.026, 139.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

#1: Protein PadR family transcriptional regulator


Mass: 21464.168 Da / Num. of mol.: 2 / Mutation: C12S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv1176c / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O50432
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 400, 0.1M Tris-HCl pH 8.5, 0.1M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.94→35 Å / Num. obs: 8284 / % possible obs: 98.5 % / Redundancy: 8.2 % / CC1/2: 0.959 / Net I/σ(I): 13.19
Reflection shellResolution: 2.94→3.05 Å / Num. unique obs: 808 / CC1/2: 0.765 / CC star: 0.931

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→30.16 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.847 / SU B: 21.933 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27023 815 9.8 %RANDOM
Rwork0.21661 ---
obs0.22196 7469 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.982 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2---1.27 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.94→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 26 16 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122784
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.6423777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3695368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84320.472127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12415400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7791526
X-RAY DIFFRACTIONr_chiral_restr0.0910.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022098
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.7064.4911481
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.5626.7211846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3634.31302
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.54558.0434158
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4714 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.94→3.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.536 47 -
Rwork0.401 471 -
obs--84.5 %

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