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- PDB-6o5c: X-ray crystal structure of metal-dependent transcriptional regula... -

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Basic information

Entry
Database: PDB / ID: 6o5c
TitleX-ray crystal structure of metal-dependent transcriptional regulator MtsR
ComponentsPutative metal-dependent transcriptional regulator
KeywordsDNA BINDING PROTEIN / Manganese / Transcription Regulator
Function / homology
Function and homology information


transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter FeoA domain / Ferrous iron transporter, core domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor ...FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter FeoA domain / Ferrous iron transporter, core domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Putative metal-dependent transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDo, H. / Kumaraswami, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109096-01A1 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence.
Authors: Do, H. / Makthal, N. / Chandrangsu, P. / Olsen, R.J. / Helmann, J.D. / Musser, J.M. / Kumaraswami, M.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative metal-dependent transcriptional regulator
B: Putative metal-dependent transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7247
Polymers50,3982
Non-polymers3265
Water18010
1
A: Putative metal-dependent transcriptional regulator
hetero molecules

B: Putative metal-dependent transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7247
Polymers50,3982
Non-polymers3265
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/41
Buried area2210 Å2
ΔGint-25 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.904, 67.904, 293.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative metal-dependent transcriptional regulator


Mass: 25198.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M3 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UTK0
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40 mM sodium acetate, 0.16 M magnesium formate, 2.6 M lithium acetate, 20% PEG 2000, 66 mM ammonium sulfate, and 0.8 mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 23865 / % possible obs: 99.8 % / Redundancy: 6.1 % / Net I/σ(I): 7.9
Reflection shellResolution: 3.1→3.27 Å / Num. unique obs: 3461

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVI

5cvi


Resolution: 3.1→29.738 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 650 4.89 %RANDOM
Rwork0.2453 ---
obs0.2474 13301 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→29.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 11 10 3434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023489
X-RAY DIFFRACTIONf_angle_d0.5944719
X-RAY DIFFRACTIONf_dihedral_angle_d11.791303
X-RAY DIFFRACTIONf_chiral_restr0.022541
X-RAY DIFFRACTIONf_plane_restr0.002594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.33910.37211280.33462429X-RAY DIFFRACTION100
3.3391-3.67460.36181340.30122461X-RAY DIFFRACTION100
3.6746-4.2050.38721080.25622521X-RAY DIFFRACTION100
4.205-5.2930.27331300.23852534X-RAY DIFFRACTION100
5.293-29.73960.24971500.22492706X-RAY DIFFRACTION100

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