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- PDB-1rf4: Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tet... -

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Basic information

Entry
Database: PDB / ID: 1rf4
TitleStructural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate Bound State
Components5-enolpyruvylshikimate-3-phosphate synthase
KeywordsTRANSFERASE / shikimate pathway / EPSP synthase / S3P / Glyphosate / PEP / S. pneumoniae
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
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
Chem-SPQ / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPark, H. / Hilsenbeck, J.L. / Kim, H.J. / Shuttleworth, W.A. / Park, Y.H. / Evans, J.N. / Kang, C.
CitationJournal: Mol.Microbiol. / Year: 2004
Title: Structural studies of Streptococcus pneumoniae EPSP synthase in unliganded state, tetrahedral intermediate-bound state and S3P-GLP-bound state.
Authors: Park, H. / Hilsenbeck, J.L. / Kim, H.J. / Shuttleworth, W.A. / Park, Y.H. / Evans, J.N. / Kang, C.
History
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN SPQ IS THE FLUORINATED TETRAHEDRAL INTERMEDIATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)185,2768
Polymers183,5154
Non-polymers1,7614
Water13,926773
1
A: 5-enolpyruvylshikimate-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3192
Polymers45,8791
Non-polymers4401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5-enolpyruvylshikimate-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3192
Polymers45,8791
Non-polymers4401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5-enolpyruvylshikimate-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3192
Polymers45,8791
Non-polymers4401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5-enolpyruvylshikimate-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3192
Polymers45,8791
Non-polymers4401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.495, 149.705, 88.011
Angle α, β, γ (deg.)90.00, 91.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein
5-enolpyruvylshikimate-3-phosphate synthase


Mass: 45878.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: aroA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9S400, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical
ChemComp-SPQ / (3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FLUORO-1-(PHOSPHONOOXY)ETHYL]OXY}-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID


Mass: 440.164 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15FO14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG, EG, NaCl, Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 %PEG80001reservoir
28 %EG1reservoir
30.2 M1reservoirNaCl
40.1 Msodium pootassium phosphate1reservoirpH6.2
55 mMligand1reservoir
660 mg/mlprotein1drop
710 mMTris-HCl1droppH7.5
8100 mM1dropKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 103059 / Num. obs: 103059 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.3 Å / % possible all: 91
Reflection
*PLUS
Num. measured all: 822394 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 91 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 4712 Random 5%
Rwork0.196 --
all0.243 93405 -
obs0.214 88693 -
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12848 0 108 773 13729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_angle_deg1.81
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / Rfactor Rwork: 0.187

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