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- PDB-8umm: EPSPS TIPS K296R variant complexed with glyphosate and shikimate-... -

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Basic information

Entry
Database: PDB / ID: 8umm
TitleEPSPS TIPS 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: 2.2 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)95,8086
Polymers94,9592
Non-polymers8484
Water6,125340
1
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9043
Polymers47,4801
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9043
Polymers47,4801
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.738, 62.422, 68.031
Angle α, β, γ (deg.)86.56, 86.17, 86.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase


Mass: 47479.566 Da / Num. of mol.: 2 / Mutation: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.53 %
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: 2.2→50 Å / Num. obs: 34634 / % possible obs: 89 % / Redundancy: 3.5 % / Rpim(I) all: 0.062 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.242.60.2715020.8980.9730.1890.330.31177.7
2.24-2.282.80.28114110.8560.960.1940.3430.30872.6
2.28-2.322.90.25717240.9090.9760.1740.3120.28688.4
2.32-2.373.10.25918020.8990.9730.1690.310.32293.4
2.37-2.423.30.2418540.9120.9770.1540.2860.28393
2.42-2.483.40.22717560.9420.9850.1420.2680.30692.8
2.48-2.543.50.2218380.9450.9860.1350.2590.31293.5
2.54-2.613.70.21217940.9470.9860.1280.2480.28992
2.61-2.693.70.19717850.9590.990.1180.230.29892
2.69-2.773.70.17617690.9620.990.1060.2060.31591.4
2.77-2.873.70.15517710.9730.9930.0930.1810.33290.3
2.87-2.993.70.12817280.9790.9950.0770.150.35588.6
2.99-3.123.70.12116700.980.9950.0730.1420.38785.2
3.12-3.293.60.09814710.9870.9970.0590.1150.44175.2
3.29-3.493.70.08918120.9890.9970.0530.1040.46493
3.49-3.763.80.07518450.9920.9980.0450.0880.5295.6
3.76-4.143.80.06518290.9930.9980.0390.0760.61494
4.14-4.743.70.05718150.9940.9980.0350.0670.74292.4
4.74-5.973.70.05616640.9950.9990.0340.0660.65586
5.97-503.70.04817940.9970.9990.0290.0560.72392

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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: 2.2→44.6 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 1985 5.73 %
Rwork0.1549 --
obs0.1574 34616 88.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 52 340 6944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016715
X-RAY DIFFRACTIONf_angle_d1.0389122
X-RAY DIFFRACTIONf_dihedral_angle_d19.4992456
X-RAY DIFFRACTIONf_chiral_restr0.0581081
X-RAY DIFFRACTIONf_plane_restr0.0061170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.2254950.18811716X-RAY DIFFRACTION64
2.23-2.290.27031200.18112160X-RAY DIFFRACTION81
2.29-2.360.22791580.16522429X-RAY DIFFRACTION93
2.36-2.430.22631560.16292484X-RAY DIFFRACTION93
2.43-2.520.23821290.15422475X-RAY DIFFRACTION93
2.52-2.620.23471620.15522413X-RAY DIFFRACTION92
2.62-2.740.18911440.15182430X-RAY DIFFRACTION92
2.74-2.880.20221470.14362403X-RAY DIFFRACTION90
2.88-3.060.21391400.14222306X-RAY DIFFRACTION87
3.06-3.30.17941310.13772047X-RAY DIFFRACTION78
3.3-3.630.16191510.14552531X-RAY DIFFRACTION95
3.63-4.160.18831630.15042501X-RAY DIFFRACTION94
4.16-5.240.19211420.15662405X-RAY DIFFRACTION91
5.24-44.60.18121470.17182331X-RAY DIFFRACTION88

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