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- PDB-8zwn: Crystal structure of DNA-binding transcriptional activator EvgA f... -

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Basic information

Entry
Database: PDB / ID: 8zwn
TitleCrystal structure of DNA-binding transcriptional activator EvgA from Escherichia coli str. K-12 substr. MG1655
ComponentsDNA-binding transcriptional activator EvgA
KeywordsDNA BINDING PROTEIN / DNA-binding transcriptional activator / the two-component regulatory system / transcription
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
: / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...: / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-binding transcriptional activator EvgA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTeng, Y. / Liu, R. / Luo, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of DNA-binding transcriptional activator EvgA from Escherichia coli str. K-12 substr. MG1655
Authors: Teng, Y. / Liu, R.
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding transcriptional activator EvgA
B: DNA-binding transcriptional activator EvgA
C: DNA-binding transcriptional activator EvgA
D: DNA-binding transcriptional activator EvgA


Theoretical massNumber of molelcules
Total (without water)99,9704
Polymers99,9704
Non-polymers00
Water00
1
A: DNA-binding transcriptional activator EvgA
B: DNA-binding transcriptional activator EvgA


Theoretical massNumber of molelcules
Total (without water)49,9852
Polymers49,9852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-12 kcal/mol
Surface area18230 Å2
MethodPISA
2
C: DNA-binding transcriptional activator EvgA
D: DNA-binding transcriptional activator EvgA


Theoretical massNumber of molelcules
Total (without water)49,9852
Polymers49,9852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-12 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.378, 109.061, 106.666
Angle α, β, γ (deg.)90.00, 125.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DNA-binding transcriptional activator EvgA


Mass: 24992.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: evgA / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACZ4
Has protein modificationN

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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: 3.9 Å3/Da / Density % sol: 68.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: mixing 2 volumes of the protein (4 mg/ml in 20 mM Tris/HCl, pH 7.0, 200 mM NaCl, 1 mM TCEP) with 0.8 volume of the well solution (0.1 M Bis-Tris Propane, pH 8.5, 1.22 M Ammonium Tartrate) ...Details: mixing 2 volumes of the protein (4 mg/ml in 20 mM Tris/HCl, pH 7.0, 200 mM NaCl, 1 mM TCEP) with 0.8 volume of the well solution (0.1 M Bis-Tris Propane, pH 8.5, 1.22 M Ammonium Tartrate) and 0.2 volume of 0.1 M Betaine.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.896→46.2 Å / Num. obs: 23189 / % possible obs: 94.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.046 / Rrim(I) all: 0.12 / Net I/σ(I): 12.2
Reflection shellResolution: 2.896→3.026 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1161 / CC1/2: 0.812 / Rpim(I) all: 0.344 / Rrim(I) all: 0.92 / % possible all: 81.5

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.2 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1997 8.62 %
Rwork0.1991 --
obs0.2043 23177 67.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 0 0 6294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.555
X-RAY DIFFRACTIONf_dihedral_angle_d17.5112375
X-RAY DIFFRACTIONf_chiral_restr0.0451004
X-RAY DIFFRACTIONf_plane_restr0.0041111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.4141520.3286551X-RAY DIFFRACTION25
2.97-3.050.298371718X-RAY DIFFRACTION32
3.05-3.140.3895860.3282844X-RAY DIFFRACTION39
3.14-3.240.39990.3117984X-RAY DIFFRACTION44
3.24-3.360.3561980.28971120X-RAY DIFFRACTION50
3.36-3.490.32911270.27111285X-RAY DIFFRACTION58
3.49-3.650.36571400.2531426X-RAY DIFFRACTION64
3.65-3.840.30421410.21731588X-RAY DIFFRACTION71
3.84-4.080.25351580.20171779X-RAY DIFFRACTION79
4.08-4.40.24551870.17641943X-RAY DIFFRACTION87
4.4-4.840.21281980.16162152X-RAY DIFFRACTION96
4.84-5.540.24492160.18222242X-RAY DIFFRACTION100
5.54-6.970.26672030.18852272X-RAY DIFFRACTION100
6.97-46.20.18812210.15232276X-RAY DIFFRACTION99

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