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

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Basic information

Entry
Database: PDB / ID: 7erp
TitleThe regulatory domain of YeiE, a sulfite sensing LysR-type transcriptional regulator from Cronobacter sakazakii (sulfite-bound 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
SULFITE ION / LysR family transcriptional regulator
Similarity search - Component
Biological speciesCronobacter sakazakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 1.1Apr 3, 2024Group: 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: LysR family transcriptional regulator
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
D: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3768
Polymers93,0564
Non-polymers3204
Water4,216234
1
A: LysR family transcriptional regulator
B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6884
Polymers46,5282
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area18020 Å2
MethodPISA
2
C: LysR family transcriptional regulator
D: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6884
Polymers46,5282
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-10 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.360, 101.329, 109.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 23263.971 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: sulfite / Source: (gene. exp.) Cronobacter sakazakii (bacteria) / Gene: YeiE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9BVC9
#2: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M 2-(N-morpholino)ethanesulfonic acid (MES) pH 7.0, 6% (v/v) polyethylene glycol (PEG) 20000, 2mM Tris (2-carboxyethyl) phosphine (TCEP)

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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: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 58388 / % possible obs: 95.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 20.27 Å2 / CC star: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.026 / Net I/σ(I): 18.06
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.53 / Num. unique obs: 2956 / CC star: 0.817 / Rpim(I) all: 0.188 / % possible all: 98.8

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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: sequence based generated model

Resolution: 2.03→32.28 Å / SU ML: 0.2945 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 29.7524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2971 2009 3.81 %
Rwork0.2675 50740 -
obs0.2686 52749 86.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.56 Å2
Refinement stepCycle: LAST / Resolution: 2.03→32.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 16 234 6352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336232
X-RAY DIFFRACTIONf_angle_d0.61788446
X-RAY DIFFRACTIONf_chiral_restr0.0431981
X-RAY DIFFRACTIONf_plane_restr0.00461075
X-RAY DIFFRACTIONf_dihedral_angle_d4.879853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.2835840.31142068X-RAY DIFFRACTION50.19
2.08-2.130.37471160.33322821X-RAY DIFFRACTION68.8
2.13-2.20.31971210.34922993X-RAY DIFFRACTION72.27
2.2-2.270.46961320.42033220X-RAY DIFFRACTION78.52
2.27-2.350.29171270.3213479X-RAY DIFFRACTION83.7
2.35-2.440.31851680.28394080X-RAY DIFFRACTION98.49
2.44-2.550.30121660.27534114X-RAY DIFFRACTION99.44
2.55-2.690.29361670.27914147X-RAY DIFFRACTION99.63
2.69-2.860.31671560.27324159X-RAY DIFFRACTION99.81
2.86-3.080.29521620.27224162X-RAY DIFFRACTION99.61
3.08-3.390.31771640.26164183X-RAY DIFFRACTION99.63
3.39-3.880.29821110.23252789X-RAY DIFFRACTION66.3
3.88-4.880.27021590.2024119X-RAY DIFFRACTION96.37
4.88-32.280.22011760.22994406X-RAY DIFFRACTION99.59

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