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- PDB-4epl: Crystal Structure of Arabidopsis thaliana GH3.11 (JAR1) in Comple... -

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Basic information

Entry
Database: PDB / ID: 4epl
TitleCrystal Structure of Arabidopsis thaliana GH3.11 (JAR1) in Complex with JA-Ile
ComponentsJasmonic acid-amido synthetase JAR1
KeywordsLIGASE / ANL Adenylating Enzyme / Acyl Acid-Amido Synthetase / Adenylation
Function / homology
Function and homology information


jasmonoyl-L-amino acid ligase / jasmonoyl-L-amino acid ligase activity / regulation of response to red or far red light / cellular response to auxin stimulus / induced systemic resistance, jasmonic acid mediated signaling pathway / L-leucine binding / protein adenylylation / response to mycotoxin / response to UV-B / amino acid binding ...jasmonoyl-L-amino acid ligase / jasmonoyl-L-amino acid ligase activity / regulation of response to red or far red light / cellular response to auxin stimulus / induced systemic resistance, jasmonic acid mediated signaling pathway / L-leucine binding / protein adenylylation / response to mycotoxin / response to UV-B / amino acid binding / enzyme binding / ATP binding / cytoplasm
Similarity search - Function
: / : / GH3 family central domain / GH3 family C-terminal domain / GH3 family / GH3 family N-terminal domain
Similarity search - Domain/homology
Chem-JAI / Jasmonoyl--L-amino acid synthetase JAR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsWestfall, C.S. / Zubieta, C. / Herrmann, J. / Kapp, U. / Nanao, M.H. / Jez, J.M.
CitationJournal: Science / Year: 2012
Title: Structural basis for prereceptor modulation of plant hormones by GH3 proteins.
Authors: Westfall, C.S. / Zubieta, C. / Herrmann, J. / Kapp, U. / Nanao, M.H. / Jez, J.M.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Jasmonic acid-amido synthetase JAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3812
Polymers65,0581
Non-polymers3231
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Jasmonic acid-amido synthetase JAR1
hetero molecules

A: Jasmonic acid-amido synthetase JAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7634
Polymers130,1162
Non-polymers6472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x+1/2,-y-1/2,z1
Buried area2330 Å2
ΔGint-10 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.039, 159.024, 76.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-805-

HOH

21A-821-

HOH

31A-969-

HOH

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Components

#1: Protein Jasmonic acid-amido synthetase JAR1 / Jasmonate-amino acid synthetase JAR1 / Protein FAR-RED INSENSITIVE 219 / Protein JASMONATE RESISTANT 1


Mass: 65057.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: JAR1, FIN219, At2g46370, F11C10.6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9SKE2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-JAI / N-({(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetyl)-L-isoleucine


Mass: 323.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M tartrate, 0.1 M MOPSO, 5 mM ATP, 5 mM MgCl2, 5mM jasmonic acid, 5 mM isoleucine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 76 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→47.5 Å / Num. all: 45961 / Num. obs: 43730 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rsym value: 0.062 / Net I/σ(I): 26.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.007→47.502 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2201 5.03 %
Rwork0.169 --
obs0.171 43725 99.51 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.008 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4941 Å2-0 Å2-0 Å2
2---0.3363 Å20 Å2
3----4.1578 Å2
Refinement stepCycle: LAST / Resolution: 2.007→47.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4367 0 23 375 4765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074501
X-RAY DIFFRACTIONf_angle_d1.0256106
X-RAY DIFFRACTIONf_dihedral_angle_d13.0691668
X-RAY DIFFRACTIONf_chiral_restr0.07689
X-RAY DIFFRACTIONf_plane_restr0.004789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.007-2.05060.24841280.21152386X-RAY DIFFRACTION93
2.0506-2.09830.30221420.2092539X-RAY DIFFRACTION100
2.0983-2.15080.26411450.18122590X-RAY DIFFRACTION100
2.1508-2.2090.21581530.17682551X-RAY DIFFRACTION100
2.209-2.2740.21071220.17582600X-RAY DIFFRACTION100
2.274-2.34740.23361400.17512592X-RAY DIFFRACTION100
2.3474-2.43120.20651230.16912582X-RAY DIFFRACTION100
2.4312-2.52860.25761250.17552612X-RAY DIFFRACTION100
2.5286-2.64370.24141390.18662591X-RAY DIFFRACTION100
2.6437-2.7830.25471270.18862599X-RAY DIFFRACTION100
2.783-2.95740.22221420.19442598X-RAY DIFFRACTION100
2.9574-3.18570.22711340.18192621X-RAY DIFFRACTION100
3.1857-3.50620.19661350.16652617X-RAY DIFFRACTION100
3.5062-4.01330.18691420.14632639X-RAY DIFFRACTION100
4.0133-5.05540.15831430.1382664X-RAY DIFFRACTION100
5.0554-47.51550.20381610.17082743X-RAY DIFFRACTION99
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)
12.18470.5082-0.72121.2801-0.75112.08760.01960.27640.1789-0.14120.08320.1342-0.084-0.2465-0.09560.25130.0131-0.01770.17840.04160.179633.3654-11.9867-29.928
20.81670.2978-0.10860.8522-0.43822.25060.0199-0.08590.10140.14060.01750.035-0.1146-0.053-0.03160.21850.00640.02140.1488-0.00490.171435.082-20.4965-1.3264
31.76350.4389-0.19261.7371-0.69832.7991-0.0460.185-0.1426-0.28080.08950.08090.3186-0.2185-0.09280.239-0.0471-0.03320.23170.04640.215126.3985-24.9019-29.9557
43.51760.27130.15263.85051.23391.9150.01990.2024-0.4470.02110.0028-0.19810.06360.0969-0.00640.207-0.0120.02650.2241-0.03450.210254.4683-41.6957-19.6385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 7:135)
2X-RAY DIFFRACTION2chain 'A' and (resseq 136:338)
3X-RAY DIFFRACTION3chain 'A' and (resseq 339:424)
4X-RAY DIFFRACTION4chain 'A' and (resseq 425:575)

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