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- PDB-7fdf: The E145S mutant of the regulatory domain of YeiE, a sulfite sens... -

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Basic information

Entry
Database: PDB / ID: 7fdf
TitleThe E145S mutant of the regulatory domain of YeiE, a sulfite sensing LysR-type transcriptional regulator from Cronobacter sakazakii (sulfate-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
LysR family transcriptional regulator
Similarity search - Component
Biological speciesCronobacter sakazakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
DepositionJul 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3182
Polymers23,2221
Non-polymers961
Water1,36976
1
A: LysR family transcriptional regulator
hetero molecules

A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6364
Polymers46,4442
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area2880 Å2
ΔGint-51 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.146, 60.146, 213.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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


Mass: 23221.934 Da / Num. of mol.: 1 / Mutation: E145S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cronobacter sakazakii (bacteria) / Gene: FZH93_18715, FZI36_01190, FZI41_05255, HZZ03_13430 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9BVC9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH 7.5, 0.2M MgCl2, 19% (v/v) PEG 3350

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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: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 14880 / % possible obs: 97.1 % / Redundancy: 22.2 % / Biso Wilson estimate: 20.77 Å2 / CC1/2: 1 / Rpim(I) all: 0.016 / Rrim(I) all: 0.083 / Net I/σ(I): 36.43
Reflection shellResolution: 2.05→2.09 Å / Mean I/σ(I) obs: 5.625 / Num. unique obs: 685 / CC1/2: 0.955 / Rpim(I) all: 0.087 / Rrim(I) all: 0.429 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ERP

7erp


Resolution: 2.05→35.59 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 19.6095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2206 2323 10.06 %
Rwork0.1928 20757 -
obs0.1956 14648 85.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.33 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 5 76 1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181582
X-RAY DIFFRACTIONf_angle_d0.43072147
X-RAY DIFFRACTIONf_chiral_restr0.0408248
X-RAY DIFFRACTIONf_plane_restr0.0038274
X-RAY DIFFRACTIONf_dihedral_angle_d3.807218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.2485820.2397709X-RAY DIFFRACTION49.13
2.09-2.140.2487950.2382804X-RAY DIFFRACTION56.4
2.14-2.190.22541000.2261875X-RAY DIFFRACTION61.63
2.19-2.240.2621070.2068967X-RAY DIFFRACTION66.96
2.24-2.30.25091270.20131045X-RAY DIFFRACTION73.34
2.3-2.370.19821190.18911149X-RAY DIFFRACTION80.82
2.37-2.450.26021380.19271242X-RAY DIFFRACTION86.25
2.45-2.540.25141440.20551274X-RAY DIFFRACTION89.01
2.54-2.640.24511440.20961359X-RAY DIFFRACTION94.29
2.64-2.760.2391490.20731368X-RAY DIFFRACTION95.77
2.76-2.90.2731580.19961402X-RAY DIFFRACTION97.44
2.9-3.080.25631550.21341388X-RAY DIFFRACTION98.41
3.08-3.320.22831660.19981450X-RAY DIFFRACTION99.75
3.32-3.660.1911630.19741414X-RAY DIFFRACTION99.87
3.66-4.180.19481600.17041438X-RAY DIFFRACTION100
4.19-5.270.18031600.15731432X-RAY DIFFRACTION100
5.27-35.590.20281560.18631441X-RAY DIFFRACTION99.81

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