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- PDB-8k5q: Crystal structure of YajQ STM0435 with c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 8k5q
TitleCrystal structure of YajQ STM0435 with c-di-GMP
ComponentsYajQ
KeywordsSTRUCTURAL GENOMICS
Function / homologyProtein of unknown function DUF520 / UPF0234, N-terminal / YajQ-like superfamily / Nucleotide-binding protein YajQ-like / UPF0234-like, C-terminal / nucleotide binding / cytosol / Chem-C2E / Nucleotide-binding protein YajQ
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDai, Y. / Zhang, M. / Wang, W. / Li, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170034 China
CitationJournal: Virulence / Year: 2024
Title: A c-di-GMP binding effector STM0435 modulates flagellar motility and pathogenicity in Salmonella
Authors: Dai , Y. / Liu , R. / Yue , Y. / Song , N. / Jia , H. / Ma , Z. / Gao , X. / Zhang , M. / Yuan , X. / Liu , Q. / Liu , X. / Li , B. / Wang , W.
History
DepositionJul 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YajQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7263
Polymers18,3451
Non-polymers1,3812
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint2 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.984, 51.697, 126.267
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 YajQ


Mass: 18344.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Gene: yajQ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A636K9V1
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 291.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M Lithium acetate dihydrate

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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: 2.28→126.27 Å / Num. obs: 8194 / % possible obs: 95.1 % / Redundancy: 12.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.031 / Rrim(I) all: 0.113 / Net I/σ(I): 17.4
Reflection shellResolution: 2.28→2.42 Å / Num. unique obs: 983 / CC1/2: 0.966

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→31.57 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 389 4.78 %
Rwork0.2142 --
obs0.2171 8144 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 90 71 1450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.198
X-RAY DIFFRACTIONf_dihedral_angle_d29.154528
X-RAY DIFFRACTIONf_chiral_restr0.061214
X-RAY DIFFRACTIONf_plane_restr0.008234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.610.29331190.24322260X-RAY DIFFRACTION85
2.61-3.290.28531230.24322676X-RAY DIFFRACTION99
3.29-31.570.26561470.18982819X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.5244 Å / Origin y: 2.7785 Å / Origin z: 0.9405 Å
111213212223313233
T0.1889 Å2-0.0256 Å2-0.01 Å2-0.2519 Å2-0.0008 Å2--0.2048 Å2
L-0.1534 °20.0407 °2-1.093 °2--0.1843 °20.1071 °2--3.767 °2
S-0.0555 Å °0.0577 Å °-0.0697 Å °-0.0087 Å °0.0009 Å °0.076 Å °0.1877 Å °-0.2274 Å °0.0303 Å °
Refinement TLS groupSelection details: all

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