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- PDB-8umn: EPSPS TIPS P126S K296R variant complexed with glyphosate and shik... -

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Basic information

Entry
Database: PDB / ID: 8umn
TitleEPSPS TIPS P126S K296R variant complexed with glyphosate and shikimate-3-phosphate
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / EPSP synthase / Aromatic amino acid synthesis pathway / Plant
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
Similarity search - Function
EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta
Similarity search - Domain/homology
GLYPHOSATE / SHIKIMATE-3-PHOSPHATE / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKim, W. / Zhang, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104896 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system.
Authors: Reed, K.B. / Kim, W. / Lu, H. / Larue, C.T. / Guo, S. / Brooks, S.M. / Montez, M.R. / Wagner, J.W. / Zhang, Y.J. / Alper, H.S.
History
DepositionOct 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,25910
Polymers94,9392
Non-polymers1,3208
Water11,061614
1
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1815
Polymers47,4701
Non-polymers7124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0785
Polymers47,4701
Non-polymers6084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.319, 63.105, 69.786
Angle α, β, γ (deg.)85.36, 85.84, 85.53
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase


Mass: 47469.531 Da / Num. of mol.: 2 / Mutation: P126S, K296R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ZEAMMB73_Zm00001d045450
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1D6NVZ6

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Non-polymers , 5 types, 622 molecules

#2: Chemical ChemComp-S3P / SHIKIMATE-3-PHOSPHATE


Mass: 254.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11O8P
#3: Chemical ChemComp-GPJ / GLYPHOSATE


Mass: 170.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO5P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 86470 / % possible obs: 83.6 % / Redundancy: 2.9 % / Rpim(I) all: 0.049 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.6320.27126410.8560.960.2080.3430.30851.4
1.63-1.662.20.25933420.8760.9660.1920.3240.34763.7
1.66-1.692.40.25436860.8910.9710.1830.3150.32872.1
1.69-1.722.60.24540700.9020.9740.1730.3020.32878.1
1.72-1.762.70.23142200.9140.9770.1630.2850.32682
1.76-1.82.80.2243370.9230.980.1550.2710.36383.6
1.8-1.852.80.19642920.9370.9840.1370.240.34882.4
1.85-1.92.90.17938910.9430.9850.1240.2190.36876.2
1.9-1.952.90.1647170.9550.9880.110.1950.41691
1.95-2.0230.2847810.0590.3330.1920.3410.68591.9
2.02-2.0930.12947530.970.9920.0890.1580.47191.8
2.09-2.1730.12147160.9740.9930.0830.1470.53191.6
2.17-2.273.10.11346630.9770.9940.0760.1370.5690.2
2.27-2.393.10.10346030.9790.9950.0690.1240.66988.6
2.39-2.543.10.08544570.9870.9970.0570.1020.5986
2.54-2.743.10.07341520.9890.9970.0490.0880.65880.2
2.74-3.013.20.06249160.990.9980.0410.0750.87294.9
3.01-3.453.30.05148330.9940.9990.0330.0610.9393.9
3.45-4.343.40.04147510.9960.9990.0260.0491.25891.8
4.34-403.30.04146490.9920.9980.0260.0492.76189.7

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Processing

Software
NameVersionClassification
PHENIX(1.18rc3_3805: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.62 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1814 2000 2.31 %
Rwork0.1575 --
obs0.1581 86457 83.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 82 614 7280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096802
X-RAY DIFFRACTIONf_angle_d0.8669237
X-RAY DIFFRACTIONf_dihedral_angle_d19.1952493
X-RAY DIFFRACTIONf_chiral_restr0.0531087
X-RAY DIFFRACTIONf_plane_restr0.0051186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.2381910.21133858X-RAY DIFFRACTION54
1.64-1.680.25021190.19684994X-RAY DIFFRACTION69
1.68-1.730.22631330.25645X-RAY DIFFRACTION78
1.73-1.790.19941440.19576073X-RAY DIFFRACTION83
1.79-1.850.2081400.1855916X-RAY DIFFRACTION82
1.85-1.930.2131410.1665939X-RAY DIFFRACTION82
1.93-2.010.18051560.15766592X-RAY DIFFRACTION92
2.01-2.120.20031570.15236650X-RAY DIFFRACTION92
2.12-2.250.17841550.14946546X-RAY DIFFRACTION91
2.25-2.430.18411520.1536405X-RAY DIFFRACTION89
2.43-2.670.18291370.1535803X-RAY DIFFRACTION81
2.67-3.060.17861610.1516788X-RAY DIFFRACTION94
3.06-3.850.15251600.14316773X-RAY DIFFRACTION93
3.85-39.620.16561540.1546475X-RAY DIFFRACTION90

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