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- PDB-1mi4: Glyphosate insensitive G96A mutant EPSP synthase liganded with sh... -

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Basic information

Entry
Database: PDB / ID: 1mi4
TitleGlyphosate insensitive G96A mutant EPSP synthase liganded with shikimate-3-phosphate
Components5-enolpyruvylshikimate-3-phosphate synthase
KeywordsTRANSFERASE / inside-out alpha-beta barrel
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 / SHIKIMATE-3-PHOSPHATE / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEschenburg, S. / Healy, M.L. / Priestman, M.A. / Lushington, G.H. / Schonbrunn, E.
CitationJournal: PLANTA / Year: 2002
Title: How the mutation glycine96 to alanine confers glyphosate insensitivity to 5-enolpyruvyl shikimate-3-phosphate synthase from Escherichia coli.
Authors: Eschenburg, S. / Healy, M.L. / Priestman, M.A. / Lushington, G.H. / Schonbrunn, E.
History
DepositionAug 21, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 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 1.5Oct 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

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Assembly

Deposited unit
A: 5-enolpyruvylshikimate-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,05416
Polymers46,1561
Non-polymers89815
Water8,629479
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.760, 85.090, 87.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46155.637 Da / Num. of mol.: 1 / Mutation: G96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aroA / Plasmid: pET24D / Production host: Escherichia coli (E. coli)
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.04 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris1droppH7.8
22 mMdithiothreitol1drop
3100 mg/mlprotein1drop
42 Msodium formate1reservoirpH7.
55 mMS3P1reservoir
620 mMglyphosate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2001 / Details: confocal mirrors
RadiationMonochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. all: 47038 / Num. obs: 47038 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.346 / Num. unique all: 3815 / % possible all: 96
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 15 Å / Num. measured all: 199475
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 96 % / Num. unique obs: 3815 / Num. measured obs: 16125

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G6T

1g6t


Resolution: 1.7→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1412 -random
Rwork0.157 ---
all0.157 47038 --
obs0.157 47038 97.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.351 Å20 Å20 Å2
2--1.665 Å20 Å2
3---1.686 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 16 521 3770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0128
X-RAY DIFFRACTIONc_angle_deg1.72
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2s3p+gph+for+spp.param
X-RAY DIFFRACTION3cis_peptide.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 2.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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