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- PDB-8jbi: SteC 202-375 mutant- C276S -

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Basic information

Entry
Database: PDB / ID: 8jbi
TitleSteC 202-375 mutant- C276S
ComponentsSecreted effector kinase SteC
KeywordsTRANSFERASE / effectors / kinase / AMP
Function / homologyTransferases; Transferring phosphorus-containing groups / kinase activity / host cell cytoplasm / phosphorylation / extracellular region / ATP binding / ADENOSINE MONOPHOSPHATE / Secreted effector kinase SteC
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.356 Å
AuthorsZhang, M. / Dai, Y. / Li, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170034 China
CitationJournal: To Be Published
Title: Salmonella manipulates macrophage cytoskeleton to penetrate gut-vascular barrier and promote dissemination during infection
Authors: Zhang, M. / Dai, Y. / Li, B.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Secreted effector kinase SteC
A: Secreted effector kinase SteC
B: Secreted effector kinase SteC
C: Secreted effector kinase SteC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,43513
Polymers78,9244
Non-polymers1,5109
Water3,009167
1
D: Secreted effector kinase SteC
A: Secreted effector kinase SteC
hetero molecules

B: Secreted effector kinase SteC
C: Secreted effector kinase SteC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,43513
Polymers78,9244
Non-polymers1,5109
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y+1/2,-z+11
Buried area12010 Å2
ΔGint-94 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.998, 92.880, 88.838
Angle α, β, γ (deg.)90.00, 107.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Secreted effector kinase SteC / Salmonella translocated effector C


Mass: 19731.074 Da / Num. of mol.: 4 / Mutation: C276S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain 14028s / SGSC 2262) (bacteria)
Gene: steC, STM14_2050 / Production host: Escherichia coli (E. coli)
References: UniProt: D0ZIB5, Transferases; Transferring phosphorus-containing groups
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: Sodium cacodylate trihydrate, Ammonium sulfate, Magnesium sulfate heptahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.356→40.398 Å / Num. obs: 35432 / % possible obs: 96.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.022 / Net I/σ(I): 24.3
Reflection shellResolution: 2.36→2.48 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5280 / CC1/2: 0.896 / Rpim(I) all: 0.246 / Rrim(I) all: 0.724 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
STARANISO1.0.5data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.356→40.398 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1664 4.7 %
Rwork0.1949 --
obs0.1972 35390 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.356→40.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 97 167 5158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085169
X-RAY DIFFRACTIONf_angle_d1.1636966
X-RAY DIFFRACTIONf_dihedral_angle_d15.751968
X-RAY DIFFRACTIONf_chiral_restr0.078757
X-RAY DIFFRACTIONf_plane_restr0.004908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3564-2.42570.28711440.24612850X-RAY DIFFRACTION98
2.4257-2.5040.30341300.23352869X-RAY DIFFRACTION100
2.504-2.59350.27071570.22772891X-RAY DIFFRACTION100
2.5935-2.69730.2756930.23281866X-RAY DIFFRACTION65
2.6973-2.82010.31531470.22662899X-RAY DIFFRACTION100
2.8201-2.96870.27091430.20822860X-RAY DIFFRACTION100
2.9687-3.15460.31731500.21832899X-RAY DIFFRACTION100
3.1546-3.39810.25031240.20412915X-RAY DIFFRACTION100
3.3981-3.73980.23941450.19192892X-RAY DIFFRACTION100
3.7398-4.28050.19441440.17072904X-RAY DIFFRACTION100
4.2805-5.39090.21321620.16952892X-RAY DIFFRACTION100
5.3909-40.3980.24451250.19782989X-RAY DIFFRACTION100

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