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- PDB-3fk1: E. coli EPSP synthase (TIPS mutation) liganded with S3P and glyphosate -

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Basic information

Entry
Database: PDB / ID: 3fk1
TitleE. coli EPSP synthase (TIPS mutation) liganded with S3P and glyphosate
Components3-phosphoshikimate 1-carboxyvinyltransferaseEPSP synthase
KeywordsTRANSFERASE / Inside-out alpha-beta barrel / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Cytoplasm
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 / cytosol
Similarity search - Function
EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) ...EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / N-(phosphonomethyl)glycine / SHIKIMATE-3-PHOSPHATE / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSchonbrunn, E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Basis of Glyphosate Resistance Resulting from the Double Mutation Thr97 -> Ile and Pro101 -> Ser in 5-Enolpyruvylshikimate-3-phosphate Synthase from Escherichia coli.
Authors: Funke, T. / Yang, Y. / Han, H. / Healy-Fried, M. / Olesen, S. / Becker, A. / Schonbrunn, E.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,88910
Polymers46,1441
Non-polymers7459
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.886, 85.042, 87.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46143.629 Da / Num. of mol.: 1 / Fragment: EPSP synthase / Mutation: Thr97Ile, Pro101Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: aroA, b0908, JW0891 / Plasmid: pET-24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A6D3, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-S3P / SHIKIMATE-3-PHOSPHATE


Mass: 254.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11O8P
#3: Chemical ChemComp-GPF / N-(phosphonomethyl)glycine / Glyphosate


Mass: 169.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO5P
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na-formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 11, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 46727 / Num. obs: 46727 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.3
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 10 / Num. unique all: 6865 / % possible all: 91.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementStarting model: 1g6s

1g6s


Resolution: 1.7→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1169 2.4 %random
Rwork0.159 ---
obs-46727 96.7 %-
Solvent computationBsol: 39.243 Å2
Displacement parametersBiso max: 46.12 Å2 / Biso mean: 15.041 Å2 / Biso min: 3.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.638 Å20 Å20 Å2
2--2.171 Å20 Å2
3----0.533 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 26 521 3824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4631.5
X-RAY DIFFRACTIONc_scbond_it2.5642
X-RAY DIFFRACTIONc_mcangle_it1.8442
X-RAY DIFFRACTIONc_scangle_it3.6032.5
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.011
LS refinement shellHighest resolution: 1.7 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2s3p+gph+for+spp+shikimate_new.par
X-RAY DIFFRACTION3cis_peptide.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5CNS_TOPPAR:ion.param

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