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- PDB-6j0e: Structures of two ArsR As(III)-responsive repressors: implication... -

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Basic information

Entry
Database: PDB / ID: 6j0e
TitleStructures of two ArsR As(III)-responsive repressors: implications for the mechanism of derepression
ComponentsArsenic responsive repressor ArsR
KeywordsTRANSCRIPTION / ArsR / As-III complex / repressor
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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...: / 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ARSENIC / Arsenic responsive repressor ArsR
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsPrabaharan, C. / Kandavelu, P. / Packianathan, C. / Rosen, P.B. / Thiyagarajan, S.
Funding support India, United States, 4items
OrganizationGrant numberCountry
Other governmentEMR/2014/000299 India
National Institutes of Health/National Library of Medicine (NIH/NLM)R01 GM55425 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)S10_RR25528 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)S10_RR028976 United States
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structures of two ArsR As(III)-responsive transcriptional repressors: Implications for the mechanism of derepression.
Authors: Prabaharan, C. / Kandavelu, P. / Packianathan, C. / Rosen, B.P. / Thiyagarajan, S.
History
DepositionDec 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arsenic responsive repressor ArsR
B: Arsenic responsive repressor ArsR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4245
Polymers28,1562
Non-polymers2683
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-55 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.770, 46.387, 121.952
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 Arsenic responsive repressor ArsR / ArsR family transcriptional regulator


Mass: 14078.169 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A5H1ZR36*PLUS
#2: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence reference for this protein is not available at uniprot at the time of data processing. C- ...Sequence reference for this protein is not available at uniprot at the time of data processing. C-terminal HHHHHH are expression tags.

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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: 2.2 Å3/Da / Density % sol: 44.05 % / Description: elongated tetrahedral shape, strong
Crystal growTemperature: 294 K / Method: microbatch / pH: 7.5 / Details: 200mM ammonium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.04478, 1.00495
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.044781
21.004951
ReflectionResolution: 1.6→30 Å / Num. obs: 29643 / % possible obs: 87 % / Redundancy: 8 % / Biso Wilson estimate: 12.45 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.014 / Rrim(I) all: 0.04 / Rsym value: 0.038 / Χ2: 0.837 / Net I/σ(I): 15.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1315 / CC1/2: 0.951 / Rpim(I) all: 0.162 / Rrim(I) all: 0.478 / Χ2: 0.691 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→29.79 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.806 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.194 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26434 1305 4.9 %RANDOM
Rwork0.17752 ---
obs0.18174 26749 87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.733 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.6→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 10 230 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0192013
X-RAY DIFFRACTIONr_bond_other_d0.0040.021885
X-RAY DIFFRACTIONr_angle_refined_deg2.6211.9722731
X-RAY DIFFRACTIONr_angle_other_deg1.5063.0034368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46223.18288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55315342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1511515
X-RAY DIFFRACTIONr_chiral_restr0.1640.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212216
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02381
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_it2.0551.3551004
X-RAY DIFFRACTIONr_mcbond_other2.0561.3551003
X-RAY DIFFRACTIONr_mcangle_it2.292.0171253
X-RAY DIFFRACTIONr_mcangle_other2.2892.0171254
X-RAY DIFFRACTIONr_scbond_it2.41.631009
X-RAY DIFFRACTIONr_scbond_other2.3991.631010
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5612.3341476
X-RAY DIFFRACTIONr_long_range_B_refined2.82817.8822246
X-RAY DIFFRACTIONr_long_range_B_other2.64917.452193
X-RAY DIFFRACTIONr_rigid_bond_restr8.07233898
X-RAY DIFFRACTIONr_sphericity_free13.7495118
X-RAY DIFFRACTIONr_sphericity_bonded4.87353965
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 50 -
Rwork0.159 1258 -
obs--54.14 %

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