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- PDB-8elf: Structure of Get3d, a homolog of Get3, from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 8elf
TitleStructure of Get3d, a homolog of Get3, from Arabidopsis thaliana
ComponentsUncharacterized protein At1g26090, chloroplastic
KeywordsCHAPERONE / P-loop ATPase / Get3 / alpha-crystallin / plant
Function / homology
Function and homology information


plastoglobule / chloroplast / ATP binding
Similarity search - Function
ArsA, HSP20-like domain / HSP20-like domain found in ArsA / Anion-transporting ATPase-like domain / Anion-transporting ATPase / HSP20-like chaperone / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / Uncharacterized protein At1g26090, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsManu, M.S. / Barlow, A.N. / Clemons Jr., W.M. / Ramasamy, S.
Funding support United States, India, 7items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR01GM097572 United States
National Institutes of Health/Office of the DirectorR01GM125063 United States
National Institutes of Health/Office of the DirectorDP1GM105385 United States
Weston Havens Foundation United States
National Science Foundation (NSF, United States)11444469 United States
National Institutes of Health/Office of the DirectorT32GM07616 United States
Department of Biotechnology (DBT, India)BT/PR11737/BPA/118/32/2014 India
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis.
Authors: Barlow, A.N. / Manu, M.S. / Saladi, S.M. / Tarr, P.T. / Yadav, Y. / Thinn, A.M.M. / Zhu, Y. / Laganowsky, A.D. / Clemons Jr., W.M. / Ramasamy, S.
History
DepositionSep 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein At1g26090, chloroplastic
B: Uncharacterized protein At1g26090, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0638
Polymers90,1372
Non-polymers9256
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-85 kcal/mol
Surface area31120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.251, 67.050, 99.398
Angle α, β, γ (deg.)90.000, 97.810, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Uncharacterized protein At1g26090, chloroplastic


Mass: 45068.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g26090, F14G11.6, F28B23.23 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DYE4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-XP4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 591.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H60O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DMPA, phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.47
Details: Protein solution: 25 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM DTT, 1 mM MgCl2, 10% glycerol, 2 mM ADP/AMP-PNP. Reservoir solution: 50 mM sodium cacodylate (pH 5.47), 50 mM lithium sulfate, 30% PEG-4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→58.7 Å / Num. obs: 52116 / % possible obs: 99.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 39.41 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.034 / Rrim(I) all: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.863 / Num. unique obs: 16240 / Rpim(I) all: 1.037

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IGF

3igf


Resolution: 2→32.83 Å / SU ML: 0.2881 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 28.0401
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2561 2557 4.91 %
Rwork0.2135 49494 -
obs0.2156 52051 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.52 Å2
Refinement stepCycle: LAST / Resolution: 2→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 57 100 6093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266116
X-RAY DIFFRACTIONf_angle_d0.51128249
X-RAY DIFFRACTIONf_chiral_restr0.0405948
X-RAY DIFFRACTIONf_plane_restr0.00571037
X-RAY DIFFRACTIONf_dihedral_angle_d7.9881854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.37931520.34292752X-RAY DIFFRACTION99.86
2.04-2.080.3671270.36022684X-RAY DIFFRACTION98.12
2.08-2.130.35041380.3042786X-RAY DIFFRACTION100
2.13-2.170.3071540.28142699X-RAY DIFFRACTION99.93
2.17-2.230.30631450.28122764X-RAY DIFFRACTION99.79
2.23-2.290.43941520.34782652X-RAY DIFFRACTION97.06
2.29-2.360.25221400.25362763X-RAY DIFFRACTION99.93
2.36-2.430.26571530.24552707X-RAY DIFFRACTION99.9
2.43-2.520.33521210.24282759X-RAY DIFFRACTION99.97
2.52-2.620.3051280.2442798X-RAY DIFFRACTION99.86
2.62-2.740.29771620.24132694X-RAY DIFFRACTION99.3
2.74-2.880.26921530.23722767X-RAY DIFFRACTION99.83
2.88-3.060.27191480.2392745X-RAY DIFFRACTION99.79
3.06-3.30.27281480.22192765X-RAY DIFFRACTION99.66
3.3-3.630.22911360.20592751X-RAY DIFFRACTION99.28
3.63-4.160.2171260.18162757X-RAY DIFFRACTION98.33
4.16-5.230.19431460.1522795X-RAY DIFFRACTION99.66
5.24-32.830.22721280.18242856X-RAY DIFFRACTION99.4

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