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- PDB-8w6v: Structural basis of chorismate isomerization by Arabidopsis isoch... -

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Basic information

Entry
Database: PDB / ID: 8w6v
TitleStructural basis of chorismate isomerization by Arabidopsis isochorismate synthase ICS1
ComponentsIsochorismate synthase 1, chloroplastic
KeywordsISOMERASE / AtICS1 in isolation
Function / homology
Function and homology information


phylloquinone biosynthetic process / isochorismate synthase / leaf abscission / isochorismate synthase activity / negative regulation of defense response / salicylic acid biosynthetic process / systemic acquired resistance / stomatal movement / plastid / defense response to fungus ...phylloquinone biosynthetic process / isochorismate synthase / leaf abscission / isochorismate synthase activity / negative regulation of defense response / salicylic acid biosynthetic process / systemic acquired resistance / stomatal movement / plastid / defense response to fungus / response to cold / chloroplast / response to bacterium / defense response to Gram-negative bacterium / defense response to bacterium
Similarity search - Function
Isochorismate synthase MenF-like / Isochorismate synthase / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Isochorismate synthase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSu, Z.H. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32160064 China
CitationJournal: Plant Physiol. / Year: 2024
Title: Structural basis of chorismate isomerization by Arabidopsis ISOCHORISMATE SYNTHASE1.
Authors: Su, Z. / Niu, C. / Zhou, S. / Xu, G. / Zhu, P. / Fu, Q. / Zhang, Y. / Ming, Z.
History
DepositionAug 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isochorismate synthase 1, chloroplastic
B: Isochorismate synthase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,98614
Polymers118,4522
Non-polymers53512
Water20,7711153
1
A: Isochorismate synthase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4937
Polymers59,2261
Non-polymers2676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area19410 Å2
MethodPISA
2
B: Isochorismate synthase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4937
Polymers59,2261
Non-polymers2676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.228, 74.585, 103.869
Angle α, β, γ (deg.)70.65, 84.36, 89.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Isochorismate synthase 1, chloroplastic / AtIcs1 / IcsI / Enhanced disease susceptibility 16 / Eds16 / Isochorismate mutase 1 / Salicylic ...AtIcs1 / IcsI / Enhanced disease susceptibility 16 / Eds16 / Isochorismate mutase 1 / Salicylic acid induction deficient 2 / Sid2 / menF-like protein 1


Mass: 59225.750 Da / Num. of mol.: 2 / Mutation: K316R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ICS1, At1g74710, F1M20.39, F25A4.31
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9S7H8, isochorismate synthase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / Source method: isolated from a natural source / Formula: H2O
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: 3.82 Å3/Da / Density % sol: 67.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2.8M sodium formate, 0.08M sodium acetate trihydrate at pH 4.6, 0.08M sodium malonate at pH 6.0, 0.02M MES monohydrate at pH 6.0, 0.1% w/v Polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.8→19.82 Å / Num. obs: 144297 / % possible obs: 96.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 7079 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.82 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 1997 1.38 %
Rwork0.1716 --
obs0.1719 144274 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7661 0 34 1153 8848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077837
X-RAY DIFFRACTIONf_angle_d0.83810604
X-RAY DIFFRACTIONf_dihedral_angle_d6.5554756
X-RAY DIFFRACTIONf_chiral_restr0.0541185
X-RAY DIFFRACTIONf_plane_restr0.0051394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.26751370.25919980X-RAY DIFFRACTION95
1.845-1.89480.25161490.233410105X-RAY DIFFRACTION96
1.8948-1.95050.25891370.213910052X-RAY DIFFRACTION96
1.9505-2.01340.26911410.202410073X-RAY DIFFRACTION96
2.0134-2.08530.22881380.188310119X-RAY DIFFRACTION96
2.0853-2.16870.19271460.183910091X-RAY DIFFRACTION96
2.1687-2.26730.22241490.178610135X-RAY DIFFRACTION96
2.2673-2.38660.21181430.179410134X-RAY DIFFRACTION96
2.3866-2.53590.20081360.180910244X-RAY DIFFRACTION97
2.5359-2.73120.20651440.180610200X-RAY DIFFRACTION97
2.7312-3.00520.20621380.180510258X-RAY DIFFRACTION98
3.0052-3.43810.17511460.161610206X-RAY DIFFRACTION97
3.4381-4.32430.13891420.138910321X-RAY DIFFRACTION98
4.3243-19.820.16331510.144910359X-RAY DIFFRACTION98

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