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- PDB-3fk0: E. coli EPSP synthase (TIPS mutation) liganded with S3P -

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Basic information

Database: PDB / ID: 3fk0
TitleE. coli EPSP synthase (TIPS mutation) liganded with S3P
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 / cytosol
3-phosphoshikimate 1-carboxyvinyltransferase / Enolpyruvate transferase domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / EPSP synthase signature 1. / EPSP synthase signature 2.
3-phosphoshikimate 1-carboxyvinyltransferase
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.
Validation Report
SummaryFull reportAbout validation report
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

Structure visualization

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

Theoretical massNumber of molelcules
Total (without water)46,81211

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.491, 84.705, 87.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121


#1: Protein/peptide 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

Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2 / Formic acid
#4: Water ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O / Water

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na-formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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 15, 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: 47294 / Num. obs: 47294 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.029 / Net I/σ(I): 30.4
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 12.5 / Num. unique all: 7239 / % possible all: 98.2


PDB_EXTRACT3.006data extraction
CrystalCleardata collection
XDSdata reduction
XDSdata scaling
RefinementStarting model: 1g6t
Resolution: 1.7→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1183 2.5 %random
Rwork0.163 ---
Obs-47294 99.6 %-
Solvent computationBsol: 38.913 Å2
Displacement parametersBiso max: 47.82 Å2 / Biso mean: 16.097 Å2 / Biso min: 4.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.853 Å20 Å20 Å2
2--2.414 Å20 Å2
3---1.44 Å2
Refine analyze
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 16 551 3823
Refine LS restraints


TypeDev idealDev ideal target
LS refinement shellHighest resolution: 1.7 Å
Xplor file
Refinement-IDSerial noParam file
X-RAY DIFFRACTION2s3p+gph+for+spp+shikimate_new.par
X-RAY DIFFRACTION3cis_peptide.param

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