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- PDB-1rf5: Structural Studies of Streptococcus pneumoniae EPSP Synthase in U... -

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Basic information

Entry
Database: PDB / ID: 1rf5
TitleStructural Studies of Streptococcus pneumoniae EPSP Synthase in Unliganded 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
3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)183,5154
Polymers183,5154
Non-polymers00
Water13,818767
1
A: 5-enolpyruvylshikimate-3-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)45,8791
Polymers45,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5-enolpyruvylshikimate-3-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)45,8791
Polymers45,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5-enolpyruvylshikimate-3-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)45,8791
Polymers45,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5-enolpyruvylshikimate-3-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)45,8791
Polymers45,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.592, 116.482, 176.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, NaCl, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
160 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
3100 mM1dropKCl
41.6 Mammonium sulfate1reservoir
50.1 M1reservoirNaCl
60.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.992, 0.980, 0.9183
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2001
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9921
20.981
30.91831
ReflectionResolution: 2.2→30 Å / Num. all: 102641 / Num. obs: 102641 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.3 Å / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 982621 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.128

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The peptide bond distance between GLU 340 and THR 341 of chains A and C, and between GLU 334 and GLU 335 of chain C, are slightly longer than typical peptide bond distance. Residues 335-340 ...Details: The peptide bond distance between GLU 340 and THR 341 of chains A and C, and between GLU 334 and GLU 335 of chain C, are slightly longer than typical peptide bond distance. Residues 335-340 were set to 0 occupancy and was not included in refinement.
RfactorNum. reflectionSelection details
Rfree0.277 5011 Random 5%
Rwork0.218 --
all0.232 98347 -
obs0.2209 95252 -
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12848 0 0 767 13615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.19
X-RAY DIFFRACTIONx_bond_d0.047
Refinement
*PLUS
Num. reflection all: 95252 / % reflection Rfree: 5 % / Rfactor Rfree: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.49
LS refinement shell
*PLUS
Rfactor Rfree: 0.272 / Rfactor Rwork: 0.219

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