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- PDB-7m0o: DGT-28 EPSPS -

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Basic information

Entry
Database: PDB / ID: 7m0o
TitleDGT-28 EPSPS
Components3-phosphoshikimate 1-carboxyvinyltransferaseEPSP synthase
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / 5-Enolpyruvylshikimate-3-Phosphate Synthase / EPSPS
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
Similarity search - Function
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
: / PHOSPHATE ION / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesStreptomyces sviceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsChekan, J.R. / Nair, S.K.
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Characterization of a Glyphosate-Tolerant Enzyme from Streptomyces svecius : A Distinct Class of 5-Enolpyruvylshikimate-3-phosphate Synthases.
Authors: Griffin, S.L. / Chekan, J.R. / Lira, J.M. / Robinson, A.E. / Yerkes, C.N. / Siehl, D.L. / Wright, T.R. / Nair, S.K. / Cicchillo, R.M.
History
DepositionMar 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5613
Polymers43,4271
Non-polymers1342
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.270, 56.720, 152.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase / EPSP synthase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / EPSPS


Mass: 43427.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sviceus (bacteria) / Gene: aroA / Production host: Escherichia coli (E. coli)
References: UniProt: B5HND8, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 1.2M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.62→76.095 Å / Num. obs: 44171 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 16.51 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.048 / Net I/σ(I): 17.1
Reflection shellResolution: 1.62→1.648 Å / Redundancy: 8 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2154 / CC1/2: 0.783 / Rpim(I) all: 0.47 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GGA

2gga


Resolution: 1.62→38.02 Å / SU ML: 0.1876 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 2037 4.85 %
Rwork0.1935 39968 -
obs0.195 42005 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.5 Å2
Refinement stepCycle: LAST / Resolution: 1.62→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 6 452 3443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683073
X-RAY DIFFRACTIONf_angle_d0.83354188
X-RAY DIFFRACTIONf_chiral_restr0.0528478
X-RAY DIFFRACTIONf_plane_restr0.0062559
X-RAY DIFFRACTIONf_dihedral_angle_d4.34542501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.31241160.23542748X-RAY DIFFRACTION100
1.66-1.70.28411480.2162774X-RAY DIFFRACTION100
1.7-1.750.26341410.19982742X-RAY DIFFRACTION100
1.75-1.80.23641490.19892759X-RAY DIFFRACTION99.97
1.8-1.850.20831330.19862777X-RAY DIFFRACTION99.97
1.85-1.920.2914960.28981971X-RAY DIFFRACTION73.4
1.92-20.3641990.27491961X-RAY DIFFRACTION75.1
2-2.090.2331380.19222827X-RAY DIFFRACTION99.97
2.09-2.20.21311480.19022762X-RAY DIFFRACTION100
2.2-2.340.29541310.2262362X-RAY DIFFRACTION85.17
2.34-2.520.25581390.19352802X-RAY DIFFRACTION99.97
2.52-2.770.24581480.19482824X-RAY DIFFRACTION99.97
2.77-3.170.20171630.18812810X-RAY DIFFRACTION99.97
3.17-3.990.16131452821X-RAY DIFFRACTION98.08
3.99-38.020.20361430.16493028X-RAY DIFFRACTION99.75

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