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- PDB-7y9i: Complex structure of AtYchF1 with ppGpp -

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Basic information

Entry
Database: PDB / ID: 7y9i
TitleComplex structure of AtYchF1 with ppGpp
ComponentsObg-like ATPase 1
KeywordsHYDROLASE / AtYchF1 / GTP-BINDING PROTEIN / ppGpp / YchF-type / P-Loop NTPase
Function / homology
Function and homology information


negative regulation of response to salt stress / plasmodesma / ribosomal large subunit binding / response to salt stress / defense response / GTP binding / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding ...negative regulation of response to salt stress / plasmodesma / ribosomal large subunit binding / response to salt stress / defense response / GTP binding / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS domain profile. / TGS / TGS-like / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. ...Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS domain profile. / TGS / TGS-like / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / Beta-grasp domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / Obg-like ATPase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsLi, X. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071210 China
Citation
Journal: Front Mol Biosci / Year: 2022
Title: Co-crystalization reveals the interaction between AtYchF1 and ppGpp.
Authors: Cheung, M.Y. / Li, X. / Ku, Y.S. / Chen, Z. / Lam, H.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses
Authors: Cheung, M.-Y. / Li, X. / Miao, R. / Fong, Y.-H. / Li, K.-P. / Yung, Y.-L. / Yu, M.-H. / Wong, K.-B. / Chen, Z. / Lam, M.-H.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: 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: Obg-like ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1633
Polymers44,5361
Non-polymers6272
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-16 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.460, 111.500, 52.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Obg-like ATPase 1 / Ribosome-binding ATPase YchF / AtYchF1


Mass: 44536.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: YchF1, At1g30580, T5I8.3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SA73, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: PEG

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.07→50.01 Å / Num. obs: 26569 / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.028 / Net I/σ(I): 18.8
Reflection shellResolution: 2.07→2.12 Å / Num. unique obs: 1922 / Rpim(I) all: 0.392

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EE0

5ee0


Resolution: 2.07→50.005 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.971 / SU ML: 0.149 / Cross valid method: NONE / ESU R: 0.199 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2355 1367 5.154 %
Rwork0.2056 25155 -
all0.207 --
obs-26522 99.853 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.867 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å2-0 Å2
2---0.066 Å20 Å2
3---2.696 Å2
Refinement stepCycle: LAST / Resolution: 2.07→50.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 37 61 2883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132885
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172701
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.6583925
X-RAY DIFFRACTIONr_angle_other_deg1.2531.5846182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5215360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3222.029138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22315463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7271517
X-RAY DIFFRACTIONr_chiral_restr0.0590.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023239
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
X-RAY DIFFRACTIONr_nbd_refined0.1890.2522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.22266
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21418
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21297
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.268
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.213
X-RAY DIFFRACTIONr_nbd_other0.1770.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.24
X-RAY DIFFRACTIONr_mcbond_it3.085.1491446
X-RAY DIFFRACTIONr_mcbond_other3.085.1461445
X-RAY DIFFRACTIONr_mcangle_it4.3397.7131804
X-RAY DIFFRACTIONr_mcangle_other4.3387.7151805
X-RAY DIFFRACTIONr_scbond_it3.6755.4871439
X-RAY DIFFRACTIONr_scbond_other3.6735.4871438
X-RAY DIFFRACTIONr_scangle_it5.6188.0812121
X-RAY DIFFRACTIONr_scangle_other5.6188.0822122
X-RAY DIFFRACTIONr_lrange_it6.85160.0393098
X-RAY DIFFRACTIONr_lrange_other6.82860.0063092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.07-2.1240.348970.32718210.32819230.6620.70799.740.308
2.124-2.1820.339930.29517880.29718840.7160.76199.84080.27
2.182-2.2450.3351060.28617030.28818110.7690.80899.88960.253
2.245-2.3140.271790.26817060.26917890.8570.84599.77640.234
2.314-2.390.316800.25316390.25617200.8440.87799.94190.223
2.39-2.4730.258940.24515890.24516850.8860.90199.88130.213
2.473-2.5660.349820.25115290.25516130.8710.90699.8760.216
2.566-2.6710.276720.24614790.24815540.9050.91299.8070.219
2.671-2.7890.312710.23514390.23915100.90.9241000.205
2.789-2.9250.204660.22113560.2214250.9340.93499.78950.198
2.925-3.0830.232770.23713040.23613820.9140.91799.92760.221
3.083-3.2690.292660.22512240.22812920.8970.92399.84520.217
3.269-3.4930.277670.21311600.21712280.9130.93999.91860.212
3.493-3.7720.221640.19910780.20111420.9440.9541000.204
3.772-4.1290.184560.179990.17110550.9680.9671000.183
4.129-4.6130.175690.1459020.1479720.9690.97699.89710.166
4.613-5.3190.235470.1548280.1588750.9470.9721000.181
5.319-6.4960.17380.2197000.2167380.9530.9491000.251
6.496-9.110.209280.1995640.1995930.9580.95999.83140.248
9.11-50.0050.234150.1673470.173670.9570.97498.63760.232

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