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- PDB-9ilw: Crystal structure of the periplasmic domain of sensor protein Evg... -

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Basic information

Entry
Database: PDB / ID: 9ilw
TitleCrystal structure of the periplasmic domain of sensor protein EvgS from Escherichia coli str. K-12 substr. MG1655
ComponentsAcid-sensing system histidine kinase EvgS
KeywordsSIGNALING PROTEIN / two-component regulatory system / sensor kinase / signal transduction / periplasm
Function / homology: / : / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / cell envelope / kinase activity / plasma membrane / Acid-sensing system histidine kinase EvgS
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTeng, Y. / Liu, R. / Luo, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the periplasmic domain of sensor protein EvgS from Escherichia coli str. K-12 substr. MG1655
Authors: Teng, Y. / Liu, R. / Luo, B.
History
DepositionJul 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acid-sensing system histidine kinase EvgS
B: Acid-sensing system histidine kinase EvgS


Theoretical massNumber of molelcules
Total (without water)116,8362
Polymers116,8362
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-6 kcal/mol
Surface area43060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.560, 109.914, 118.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acid-sensing system histidine kinase EvgS


Mass: 58418.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: evgS, GP975_24990 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T5ZJL6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1 volume of the protein solution (18 mg/ml in 20 mM Tris/HCl, 200 mM NaCl, pH 8.0) was then mixed with 1 volume of reservoir solution (28% w/v Polyethylene glycol 4,000, 0.1 M TRIS, 0.8 M ...Details: 1 volume of the protein solution (18 mg/ml in 20 mM Tris/HCl, 200 mM NaCl, pH 8.0) was then mixed with 1 volume of reservoir solution (28% w/v Polyethylene glycol 4,000, 0.1 M TRIS, 0.8 M lithium chloride, pH 8.5) .

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→39.87 Å / Num. obs: 31375 / % possible obs: 99.9 % / Redundancy: 9.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.088 / Rrim(I) all: 0.27 / Net I/σ(I): 10.7
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4115 / CC1/2: 0.726 / Rpim(I) all: 0.403 / Rrim(I) all: 1.237

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→39.867 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1568 5 %
Rwork0.2044 --
obs0.207 31366 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→39.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7929 0 0 95 8024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038124
X-RAY DIFFRACTIONf_angle_d0.59411083
X-RAY DIFFRACTIONf_dihedral_angle_d2.8494909
X-RAY DIFFRACTIONf_chiral_restr0.0421267
X-RAY DIFFRACTIONf_plane_restr0.0041422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78710.32121420.27852668X-RAY DIFFRACTION100
2.7871-2.88670.32721360.26622675X-RAY DIFFRACTION100
2.8867-3.00230.29851500.26482654X-RAY DIFFRACTION100
3.0023-3.13890.30181570.25142655X-RAY DIFFRACTION100
3.1389-3.30430.32131280.23142712X-RAY DIFFRACTION100
3.3043-3.51120.25861430.22762677X-RAY DIFFRACTION100
3.5112-3.78210.28361380.19532706X-RAY DIFFRACTION100
3.7821-4.16230.20691340.18072717X-RAY DIFFRACTION100
4.1623-4.76380.22361700.16442709X-RAY DIFFRACTION100
4.7638-5.99860.22641200.18482767X-RAY DIFFRACTION100
5.9986-39.8670.2171500.17122858X-RAY DIFFRACTION99
Refinement TLS params.

T12: -0.0195 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4138-0.12560.11241.617-0.76621.58250.0365-0.01730.0320.0778-0.00810.0819-0.0371-0.0086-0.01990.16050.00540.2191-0.03630.19116.320815.9453-13.4385
21.1574-0.2408-0.00391.17290.13220.697-0.0433-0.053-0.07640.04850.01550.03620.04910.08590.02530.18380.01730.16510.02840.15916.7481-11.9894-34.0467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 26 through 534)
2X-RAY DIFFRACTION2(chain 'B' and resid 26 through 534)

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