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- PDB-9uow: Crystal structure of Gossypium hirsutum (Cotton) 5-enol-pyruvyl-s... -

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Basic information

Entry
Database: PDB / ID: 9uow
TitleCrystal structure of Gossypium hirsutum (Cotton) 5-enol-pyruvyl-shikimate-3-phosphate synthase (EPSPS) in open conformation
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / Gossypium hirsutum EPSPS Synthase
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 / chloroplast
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 / DI(HYDROXYETHYL)ETHER / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesGossypium hirsutum (cotton)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJangid, K. / Kumar, R. / Sharma, A.K. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Structural and Biochemical Insights into Cotton 5-Enolpyruvylshikimate-3-Phosphate Synthase: Toward Inhibitor Design and Glyphosate Resistance.
Authors: Jangid, K. / Chaudhary, D. / Verma, S. / Das, J. / Baksi, S. / Sharma, A.K. / Kumar, R. / Kumar, P.
History
DepositionApr 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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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
C: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,01814
Polymers145,0213
Non-polymers99711
Water3,657203
1
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,10510
Polymers48,3401
Non-polymers7659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5733
Polymers48,3401
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-phosphoshikimate 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)48,3401
Polymers48,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.855, 89.942, 116.233
Angle α, β, γ (deg.)90.00, 107.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase


Mass: 48340.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gossypium hirsutum (cotton) / Gene: LOC107945613 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1U8N867, 3-phosphoshikimate 1-carboxyvinyltransferase

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Non-polymers , 5 types, 214 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GPJ / GLYPHOSATE


Mass: 170.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.16 M calcium acetate hydrate, 0.08 M sodium cacodylate (pH 6.5), and 14.4% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.2→24.47 Å / Num. obs: 79755 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.082 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4526 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PXY

7pxy


Resolution: 2.2→24.47 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.554 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24769 3993 5 %RANDOM
Rwork0.20112 ---
obs0.20349 75646 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.285 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20.73 Å2
2---0.72 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 2.2→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9894 0 64 203 10161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01210115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169876
X-RAY DIFFRACTIONr_angle_refined_deg2.4351.82813694
X-RAY DIFFRACTIONr_angle_other_deg0.8091.74222832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26651323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.426557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.761101737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.21610
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022046
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8071.7555301
X-RAY DIFFRACTIONr_mcbond_other2.8071.7555301
X-RAY DIFFRACTIONr_mcangle_it4.2763.1446621
X-RAY DIFFRACTIONr_mcangle_other4.2763.1456622
X-RAY DIFFRACTIONr_scbond_it3.8712.1894814
X-RAY DIFFRACTIONr_scbond_other3.872.1894814
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7883.8217074
X-RAY DIFFRACTIONr_long_range_B_refined7.57117.3510622
X-RAY DIFFRACTIONr_long_range_B_other7.57217.3510612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 313 -
Rwork0.263 5503 -
obs--99.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5243-1.06670.51021.3755-0.44020.4423-0.0371-0.1584-0.03860.05850.0520.2654-0.0101-0.2121-0.01490.0159-0.00820.02660.1376-0.03580.111623.83130.159537.5939
20.62210.14891.21380.17560.54033.1403-0.0133-0.18150.1068-0.0408-0.00010.0438-0.1728-0.2350.01350.041-0.03520.04040.1126-0.01060.202452.559421.277146.3868
31.80021.25230.93371.17660.71070.842-0.04890.1667-0.2189-0.17960.0949-0.25390.06260.2503-0.0460.20350.01110.02280.19470.00830.167753.9781-21.54658.8979
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 612
2X-RAY DIFFRACTION2B79 - 605
3X-RAY DIFFRACTION3C79 - 520

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