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- PDB-7pxy: Crystal structure of Arabidopsis thaliana 5-enol-pyruvyl-shikimat... -

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Basic information

Entry
Database: PDB / ID: 7pxy
TitleCrystal structure of Arabidopsis thaliana 5-enol-pyruvyl-shikimate-3-phosphate synthase (EPSPS) in open conformation
Components3-phosphoshikimate 1-carboxyvinyltransferase, chloroplasticEPSP synthase
KeywordsPLANT PROTEIN / glyphosate / herbicide design / EPSP synthase
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chloroplast stroma / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / chloroplast
Similarity search - Function
EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta
Similarity search - Domain/homology
3-phosphoshikimate 1-carboxyvinyltransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRuszkowski, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Deciphering the structure of Arabidopsis thaliana 5- enol -pyruvyl-shikimate-3-phosphate synthase: An essential step toward the discovery of novel inhibitors to supersede glyphosate.
Authors: Ruszkowski, M. / Forlani, G.
History
DepositionOct 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: 3-phosphoshikimate 1-carboxyvinyltransferase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9323
Polymers47,8731
Non-polymers602
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.410, 108.410, 156.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1131-

HOH

21A-1159-

HOH

31A-1164-

HOH

41A-1168-

HOH

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Components

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase, chloroplastic / EPSP synthase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / AtEPSPS


Mass: 47872.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g45300, F4L23.19 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P05466, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 75% of Index G12 (0.2 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350) + 10 mM glyphosate 2+2 drop Cryoprotection: Index G12+20% ethylene glycol; 0.5 ul ...Details: 75% of Index G12 (0.2 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350) + 10 mM glyphosate 2+2 drop Cryoprotection: Index G12+20% ethylene glycol; 0.5 ul of 200 mM glyphosate was added to 10 ul of cryo solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→80 Å / Num. obs: 92087 / % possible obs: 99.9 % / Redundancy: 18.5 % / Biso Wilson estimate: 22.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14710 / CC1/2: 0.784 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nvs

3nvs


Resolution: 1.4→47.08 Å / SU ML: 0.1729 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Anisotropic refinement of ADPs,
RfactorNum. reflection% reflection
Rfree0.1898 1012 1.1 %
Rwork0.1517 91062 -
obs0.1521 92074 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.48 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 2 478 3807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093399
X-RAY DIFFRACTIONf_angle_d1.0134613
X-RAY DIFFRACTIONf_chiral_restr0.0936545
X-RAY DIFFRACTIONf_plane_restr0.0114598
X-RAY DIFFRACTIONf_dihedral_angle_d12.69661263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.470.31771420.24812812X-RAY DIFFRACTION99.66
1.47-1.560.2171430.174912872X-RAY DIFFRACTION99.98
1.56-1.680.21491440.150312915X-RAY DIFFRACTION99.99
1.68-1.850.19061440.144812946X-RAY DIFFRACTION99.99
1.85-2.120.18261440.141212976X-RAY DIFFRACTION100
2.12-2.670.20461460.162913086X-RAY DIFFRACTION99.97
2.67-47.080.17491490.144813455X-RAY DIFFRACTION99.79

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