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- PDB-7erq: The regulatory domain of YeiE, a sulfite sensing LysR-type transc... -

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Basic information

Entry
Database: PDB / ID: 7erq
TitleThe regulatory domain of YeiE, a sulfite sensing LysR-type transcriptional regulator from Cronobacter sakazakii (ligand-free form)
ComponentsLysR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / LysR-type transcriptional regulator / LTTR / Cronobacter sakazakii / sulfite
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
LysR family transcriptional regulator
Similarity search - Component
Biological speciesCronobacter sakazakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHong, S. / Ha, N.-C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Crystal structures of YeiE from Cronobacter sakazakii and the role of sulfite tolerance in gram-negative bacteria.
Authors: Hong, S. / Kim, J. / Cho, E. / Na, S. / Yoo, Y.J. / Cho, Y.H. / Ryu, S. / Ha, N.C.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,5602
Polymers46,5602
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-12 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.074, 63.074, 236.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein LysR family transcriptional regulator / Putative transcriptional regulator


Mass: 23279.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cronobacter sakazakii (bacteria) / Gene: YeiE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9BVC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Hydroxyethyl piperazineetahnesulfonic acid (HEPES) pH 7.5, 11% (v/v) PEG 10000, 6% (v/v) 2-Methyl-2,4-pentanediol (MPD), 50microM sodium selenite

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 35724 / % possible obs: 99.1 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.58 Å2 / CC star: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Net I/σ(I): 28.17
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.54 / Num. unique obs: 1625 / CC star: 0.845 / Rpim(I) all: 0.161

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ERP

7erp


Resolution: 1.95→49.28 Å / SU ML: 0.212 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 22.3939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 2892 6.11 %
Rwork0.1973 44405 -
obs0.1999 32396 71.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.83 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 0 227 3400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473239
X-RAY DIFFRACTIONf_angle_d0.76284397
X-RAY DIFFRACTIONf_chiral_restr0.0503506
X-RAY DIFFRACTIONf_plane_restr0.0068566
X-RAY DIFFRACTIONf_dihedral_angle_d17.89891223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.3197330.2797497X-RAY DIFFRACTION16.65
1.98-2.020.3049440.2769656X-RAY DIFFRACTION22.22
2.02-2.050.3244620.2793937X-RAY DIFFRACTION31.78
2.05-2.090.3077800.28331226X-RAY DIFFRACTION41.19
2.09-2.140.3085930.2711419X-RAY DIFFRACTION48.23
2.14-2.180.29241060.26311585X-RAY DIFFRACTION53.14
2.18-2.230.29611110.25461640X-RAY DIFFRACTION55.43
2.23-2.290.25371100.23181710X-RAY DIFFRACTION58.18
2.29-2.350.26491190.22641884X-RAY DIFFRACTION62.44
2.35-2.420.26491280.21151941X-RAY DIFFRACTION65.72
2.42-2.50.28631350.20662102X-RAY DIFFRACTION71.31
2.5-2.590.22621560.19452400X-RAY DIFFRACTION81.3
2.59-2.690.25861780.20842770X-RAY DIFFRACTION92.73
2.69-2.810.24761910.19572923X-RAY DIFFRACTION98.36
2.82-2.960.22671930.20082933X-RAY DIFFRACTION99.4
2.96-3.150.23761880.20582975X-RAY DIFFRACTION99.56
3.15-3.390.2591830.18812950X-RAY DIFFRACTION99.71
3.39-3.730.2181950.18232987X-RAY DIFFRACTION99.84
3.73-4.270.21671930.15782948X-RAY DIFFRACTION99.9
4.27-5.380.18492000.16252946X-RAY DIFFRACTION99.87
5.38-49.280.22731940.18592976X-RAY DIFFRACTION99.94

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