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- PDB-1q36: EPSP synthase (Asp313Ala) liganded with tetrahedral reaction inte... -

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Basic information

Entry
Database: PDB / ID: 1q36
TitleEPSP synthase (Asp313Ala) liganded with tetrahedral reaction intermediate
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / inside-out alpha-beta barrel
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase 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 / Chem-SKP / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEschenburg, S. / Kabsch, W. / Healy, M.L. / Schonbrunn, E.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: A New View of the Mechanisms of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) and 5-Enolpyruvylshikimate-3-phosphate Synthase (AroA) Derived from X-ray Structures of Their Tetrahedral ...Title: A New View of the Mechanisms of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) and 5-Enolpyruvylshikimate-3-phosphate Synthase (AroA) Derived from X-ray Structures of Their Tetrahedral Reaction Intermediate States.
Authors: Eschenburg, S. / Kabsch, W. / Healy, M.L. / Schonbrunn, E.
History
DepositionJul 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 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 1.5Aug 16, 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)46,93411
Polymers46,0981
Non-polymers83610
Water9,710539
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.810, 85.049, 87.545
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 3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / EPSPS


Mass: 46097.605 Da / Num. of mol.: 1 / Mutation: D313A
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) / Strain (production host): STBL2-DE3
References: UniProt: P0A6D3, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-SKP / 5-(1-CARBOXY-1-PHOSPHONOOXY-ETHOXYL)-4-HYDROXY-3-PHOSPHONOOXY-CYCLOHEX-1-ENECARBOXYLIC ACID / 5-(1-CARBOXY-1-PHOSPHONOOXY-ETHOXYL)-SHIKIMATE-3-PHOSPHATE


Mass: 422.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O14P2
#3: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 55905 / Num. obs: 55905 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.4
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.3 / Num. unique all: 4795 / % possible all: 95.1

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Processing

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

1g6t


Resolution: 1.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.187 1678 random
Rwork0.155 --
obs0.155 55905 -
all-55905 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.262 Å20 Å20 Å2
2--1.08 Å20 Å2
3---0.181 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 26 566 3860
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0163
X-RAY DIFFRACTIONc_angle_deg1.794
X-RAY DIFFRACTIONc_mcbond_it1.3671.5
X-RAY DIFFRACTIONc_mcangle_it1.8032
LS refinement shellResolution: 1.6→1.62 Å
RfactorNum. reflection
Rfree0.186 49
Rwork0.173 -
obs-1564
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2spp+for.par
X-RAY DIFFRACTION3cis_peptide.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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