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- PDB-8qkf: SmtB protein of Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 8qkf
TitleSmtB protein of Mycobacterium smegmatis
ComponentsArsR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / metalloregulator / ArsR/SmtB family transcriptional factor
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
: / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional repressor SmtB
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsPotocki, S. / Pyra, A. / Nowak, E. / Rola, A. / Plaskowka, K. / Trojanowski, D. / Holowka, J. / Pasikowski, P. / Gumienna-Kontecka, E. / Zakrzewska-Czerwinska, J.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2017/26/D/ST5/00372 Poland
CitationJournal: To Be Published
Title: SmtB protein of Mycobacterium smegmatis
Authors: Potocki, S. / Pyra, A. / Nowak, E. / Plaskowka, K. / Rola, A. / Trojanowski, D. / Holowka, J. / Pasikowski, P. / Gumienna-Kontecka, E. / Zakrzewska-Czerwinska, J.
History
DepositionSep 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ArsR family transcriptional regulator
B: ArsR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,3022
Polymers26,3022
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-28 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.292, 72.479, 82.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ArsR family transcriptional regulator


Mass: 13151.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: smtB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A653FM47
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: L-Proline, PEG 3350, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.88→41.11 Å / Num. obs: 21130 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.073 / Net I/σ(I): 13.25
Reflection shellResolution: 1.88→1.99 Å / Num. unique obs: 3401 / CC1/2: 0.248

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→41.11 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.564 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24351 1022 5 %RANDOM
Rwork0.19392 ---
obs0.19642 19378 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.288 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å2-0 Å20 Å2
2---0.37 Å20 Å2
3----1.49 Å2
Refinement stepCycle: 1 / Resolution: 1.88→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 0 101 1587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191508
X-RAY DIFFRACTIONr_bond_other_d0.0010.021545
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9752051
X-RAY DIFFRACTIONr_angle_other_deg0.91833527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6685191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35723.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5291516
X-RAY DIFFRACTIONr_chiral_restr0.1140.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02327
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_it4.8575.159770
X-RAY DIFFRACTIONr_mcbond_other4.7485.153769
X-RAY DIFFRACTIONr_mcangle_it6.3897.692959
X-RAY DIFFRACTIONr_mcangle_other6.3877.703960
X-RAY DIFFRACTIONr_scbond_it7.0666.304738
X-RAY DIFFRACTIONr_scbond_other7.0536.288736
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.0369.0871092
X-RAY DIFFRACTIONr_long_range_B_refined13.35942.2461652
X-RAY DIFFRACTIONr_long_range_B_other13.36842.2091641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.928 Å
RfactorNum. reflection% reflection
Rfree0.602 54 -
Rwork0.605 1027 -
obs--68.59 %

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