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- PDB-8w71: Structural basis of chorismate isomerization by Arabidopsis isoch... -

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Basic information

Entry
Database: PDB / ID: 8w71
TitleStructural basis of chorismate isomerization by Arabidopsis isochorismate synthase ICS1
ComponentsIsochorismate synthase 1, chloroplastic
KeywordsISOMERASE / chorismate-bound AtICS1 complex
Function / homology
Function and homology information


leaf abscission / negative regulation of defense response / isochorismate synthase / isochorismate synthase activity / systemic acquired resistance / phylloquinone biosynthetic process / salicylic acid biosynthetic process / stomatal movement / plastid / defense response to fungus ...leaf abscission / negative regulation of defense response / isochorismate synthase / isochorismate synthase activity / systemic acquired resistance / phylloquinone biosynthetic process / salicylic acid biosynthetic process / 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
FORMIC ACID / Chem-ISJ / Isochorismate synthase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.121 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 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)119,0458
Polymers118,4522
Non-polymers5936
Water13,836768
1
A: Isochorismate synthase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5224
Polymers59,2261
Non-polymers2973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-8 kcal/mol
Surface area19450 Å2
MethodPISA
2
B: Isochorismate synthase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5224
Polymers59,2261
Non-polymers2973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-10 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.103, 73.901, 103.784
Angle α, β, γ (deg.)70.84, 84.46, 90.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Isochorismate synthase 1, chloroplastic /


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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9S7H8
#2: Chemical ChemComp-ISJ / (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid / Chorismic Acid / Chorismic acid


Mass: 226.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2.8M sodium formate, 0.08M sodium acetate trihydrate at pH 4.6, 0.02M magnesium formate dihydrate, 3% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.12→68.41 Å / Num. obs: 84255 / % possible obs: 93.4 % / Redundancy: 2.2 % / CC1/2: 0.965 / Rmerge(I) obs: 0.075 / Net I/σ(I): 5.4
Reflection shellResolution: 2.12→2.24 Å / Rmerge(I) obs: 0.248 / Num. unique obs: 12284 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.121→39.03 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 4227 5.02 %
Rwork0.1796 --
obs0.1811 84205 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.121→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7661 0 40 768 8469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087851
X-RAY DIFFRACTIONf_angle_d0.90710636
X-RAY DIFFRACTIONf_dihedral_angle_d3.3524758
X-RAY DIFFRACTIONf_chiral_restr0.0541193
X-RAY DIFFRACTIONf_plane_restr0.0061396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1212-2.14530.31971420.23412540X-RAY DIFFRACTION92
2.1453-2.17050.27511390.23072703X-RAY DIFFRACTION93
2.1705-2.1970.24091430.21412699X-RAY DIFFRACTION94
2.197-2.22480.20331470.20992692X-RAY DIFFRACTION94
2.2248-2.25410.24361410.21532632X-RAY DIFFRACTION94
2.2541-2.2850.24151390.19482757X-RAY DIFFRACTION95
2.285-2.31760.19231390.20122654X-RAY DIFFRACTION95
2.3176-2.35220.2361580.20152759X-RAY DIFFRACTION95
2.3522-2.38890.27581740.19932679X-RAY DIFFRACTION95
2.3889-2.42810.21321510.19832677X-RAY DIFFRACTION95
2.4281-2.470.23281370.20272749X-RAY DIFFRACTION94
2.47-2.51490.22351310.19642712X-RAY DIFFRACTION95
2.5149-2.56320.22911350.19972659X-RAY DIFFRACTION94
2.5632-2.61550.24341170.20532768X-RAY DIFFRACTION95
2.6155-2.67240.28151360.2042662X-RAY DIFFRACTION94
2.6724-2.73460.22621650.19632694X-RAY DIFFRACTION93
2.7346-2.80290.26741480.20862588X-RAY DIFFRACTION93
2.8029-2.87870.22361360.20342695X-RAY DIFFRACTION93
2.8787-2.96340.23261380.19732669X-RAY DIFFRACTION94
2.9634-3.0590.24181280.20522689X-RAY DIFFRACTION94
3.059-3.16830.22791530.19822666X-RAY DIFFRACTION93
3.1683-3.2950.20721650.1762622X-RAY DIFFRACTION94
3.295-3.44490.2031570.16912689X-RAY DIFFRACTION94
3.4449-3.62640.19461620.16112654X-RAY DIFFRACTION93
3.6264-3.85340.17631060.15262699X-RAY DIFFRACTION93
3.8534-4.15070.18211280.14712660X-RAY DIFFRACTION92
4.1507-4.56780.16781320.13132611X-RAY DIFFRACTION91
4.5678-5.22740.1621370.14542613X-RAY DIFFRACTION91
5.2274-6.58090.19541160.17852550X-RAY DIFFRACTION89
6.5809-39.030.15231270.15752537X-RAY DIFFRACTION88

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