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- PDB-6uvu: Crystal structure of the AntR antimony-specific transcriptional r... -

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Basic information

Entry
Database: PDB / ID: 6uvu
TitleCrystal structure of the AntR antimony-specific transcriptional repressor
ComponentsArsR family transcriptional regulator
KeywordsTRANSCRIPTION / ArsR / Arsenic/Antimony Binding / transcriptional repressor
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Helix-turn-helix domain / : / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ArsR family transcriptional regulator
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsThiruselvam, V. / Banumathi, S. / Palani, K. / Manohar, R. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM055425 United States
CitationJournal: Mol.Microbiol. / Year: 2021
Title: Functional and structural characterization of AntR, an Sb(III) responsive transcriptional repressor.
Authors: Viswanathan, T. / Chen, J. / Wu, M. / An, L. / Kandavelu, P. / Sankaran, B. / Radhakrishnan, M. / Li, M. / Rosen, B.P.
History
DepositionNov 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
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 / _citation.year
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,0702
Polymers27,0702
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-41 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.690, 58.510, 53.490
Angle α, β, γ (deg.)90.000, 118.280, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein ArsR family transcriptional regulator


Mass: 13534.821 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Gene: P353_26355 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A096F4H2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.55 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000, 0.1 M TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.1→47.11 Å / Num. obs: 16526 / % possible obs: 98 % / Redundancy: 2 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.06 / Net I/σ(I): 13.87
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.62 / Num. unique obs: 1653 / CC1/2: 0.95 / Rrim(I) all: 0.21

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Processing

Software
NameVersionClassification
REFMAC1.13_2998refinement
PHENIX1.13_2998refinement
iMOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1smt

1smt


Resolution: 2.1→47.11 Å / SU ML: 0.2912 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.063
RfactorNum. reflection% reflection
Rfree0.2625 872 5.33 %
Rwork0.2216 --
obs0.224 16347 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.66 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 0 111 1812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721713
X-RAY DIFFRACTIONf_angle_d0.94992312
X-RAY DIFFRACTIONf_chiral_restr0.0541283
X-RAY DIFFRACTIONf_plane_restr0.0047302
X-RAY DIFFRACTIONf_dihedral_angle_d15.41991076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.29831020.2692621X-RAY DIFFRACTION99.16
2.23-2.40.35621280.29832467X-RAY DIFFRACTION95.12
2.4-2.650.311660.2382581X-RAY DIFFRACTION100
2.65-3.030.34521420.25712576X-RAY DIFFRACTION99.16
3.03-3.820.27351500.21512613X-RAY DIFFRACTION99.68
3.82-47.110.20291840.17882617X-RAY DIFFRACTION99.5

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