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- PDB-4eql: Crystal Structure of GH3.12 in complex with AMP and salicylate -

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Basic information

Entry
Database: PDB / ID: 4eql
TitleCrystal Structure of GH3.12 in complex with AMP and salicylate
Components4-substituted benzoates-glutamate ligase GH3.12
KeywordsLIGASE / firefly luciferase family / acyl adenylase / amino acid conjugation
Function / homology
Function and homology information


4-aminobenzoate amino acid synthetase activity / benzoate amino acid synthetase activity / vanillate amino acid synthetase activity / 4-hydroxybenzoate amino acid synthetase activity / positive regulation of plant-type hypersensitive response / salicylic acid mediated signaling pathway / benzoate metabolic process / regulation of systemic acquired resistance / detection of fungus / plant-type hypersensitive response ...4-aminobenzoate amino acid synthetase activity / benzoate amino acid synthetase activity / vanillate amino acid synthetase activity / 4-hydroxybenzoate amino acid synthetase activity / positive regulation of plant-type hypersensitive response / salicylic acid mediated signaling pathway / benzoate metabolic process / regulation of systemic acquired resistance / detection of fungus / plant-type hypersensitive response / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / defense response / cellular response to hypoxia / defense response to bacterium
Similarity search - Function
GH3 family / GH3 auxin-responsive promoter
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 2-HYDROXYBENZOIC ACID / 4-substituted benzoates-glutamate ligase GH3.12
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWestfall, C. / Zubieta, C. / Nanao, M. / Herrmann, J. / Jez, J.
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 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: 4-substituted benzoates-glutamate ligase GH3.12
B: 4-substituted benzoates-glutamate ligase GH3.12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,4966
Polymers131,5252
Non-polymers9714
Water21,0961171
1
A: 4-substituted benzoates-glutamate ligase GH3.12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2483
Polymers65,7621
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-substituted benzoates-glutamate ligase GH3.12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2483
Polymers65,7621
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-7 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.420, 66.580, 101.000
Angle α, β, γ (deg.)90.00, 106.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 4-substituted benzoates-glutamate ligase GH3.12 / Auxin-responsive GH3-like protein 12 / AtGH3-12 / Protein GH3-LIKE DEFENSE GENE 1 / Protein ...Auxin-responsive GH3-like protein 12 / AtGH3-12 / Protein GH3-LIKE DEFENSE GENE 1 / Protein GRETCHEN HAGEN 3.12 / Protein HOPW1-1-INTERACTING 3 / Protein avrPPHB SUSCEPTIBLE 3


Mass: 65762.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: GH3.12, GDG1, PBS3, WIN3, At5g13320, T22N19.5, T31B5.140
Production host: Escherichia coli (E. coli)
References: UniProt: Q9LYU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1171 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG3350, 0.25M ammonium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.8→96 Å / Num. all: 108026 / Num. obs: 106773 / % possible obs: 98.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 3.7 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.185 / Net I/σ(I): 9.9
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.914 / Mean I/σ(I) obs: 1.9 / Num. unique all: 17474 / % possible all: 98.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EQ4

4eq4


Resolution: 1.8→50.285 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 5313 4.98 %random
Rwork0.1767 ---
obs0.1781 106717 98.85 %-
all-108026 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.986 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1807 Å20 Å20.461 Å2
2--0.1564 Å20 Å2
3---0.0243 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7749 0 66 1171 8986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088082
X-RAY DIFFRACTIONf_angle_d1.06710994
X-RAY DIFFRACTIONf_dihedral_angle_d13.123021
X-RAY DIFFRACTIONf_chiral_restr0.0721235
X-RAY DIFFRACTIONf_plane_restr0.0041402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.33551810.31663310X-RAY DIFFRACTION99
1.8205-1.84190.35341680.29863312X-RAY DIFFRACTION98
1.8419-1.86430.28161580.27313415X-RAY DIFFRACTION99
1.8643-1.88790.28191680.24713347X-RAY DIFFRACTION98
1.8879-1.91280.25271800.22823327X-RAY DIFFRACTION98
1.9128-1.9390.25521690.21563373X-RAY DIFFRACTION99
1.939-1.96670.24572050.21013282X-RAY DIFFRACTION98
1.9667-1.99610.23131900.19763377X-RAY DIFFRACTION99
1.9961-2.02720.22561780.19263368X-RAY DIFFRACTION98
2.0272-2.06050.26732060.18953335X-RAY DIFFRACTION99
2.0605-2.0960.22761730.18813355X-RAY DIFFRACTION98
2.096-2.13410.20371950.18063358X-RAY DIFFRACTION99
2.1341-2.17520.24421800.1723370X-RAY DIFFRACTION99
2.1752-2.21960.19981850.1683364X-RAY DIFFRACTION98
2.2196-2.26780.2091840.15733340X-RAY DIFFRACTION100
2.2678-2.32060.19651950.16713349X-RAY DIFFRACTION99
2.3206-2.37860.21241610.15773396X-RAY DIFFRACTION99
2.3786-2.44290.20661890.16373369X-RAY DIFFRACTION100
2.4429-2.51480.21481580.1663419X-RAY DIFFRACTION99
2.5148-2.5960.19981720.16343382X-RAY DIFFRACTION99
2.596-2.68880.2141710.17173428X-RAY DIFFRACTION99
2.6888-2.79640.19611500.16593392X-RAY DIFFRACTION99
2.7964-2.92370.18231570.16633412X-RAY DIFFRACTION99
2.9237-3.07780.18731680.16693419X-RAY DIFFRACTION99
3.0778-3.27060.19361770.16833419X-RAY DIFFRACTION99
3.2706-3.52310.18151840.15733400X-RAY DIFFRACTION99
3.5231-3.87750.15661740.14423409X-RAY DIFFRACTION99
3.8775-4.43830.16161840.14163418X-RAY DIFFRACTION99
4.4383-5.59060.18551750.16623442X-RAY DIFFRACTION99
5.5906-50.30420.21111780.21873517X-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)
11.1033-0.05530.17190.1770.08560.29450.0209-0.0466-0.0410.0615-0.0174-0.00830.0455-0.011-0.00490.1122-0.010.00180.08410.01230.098235.503313.02035.9228
23.31370.6782-0.87423.3842-0.69273.33320.1754-0.6074-0.18910.3592-0.03540.2870.1441-0.42-0.09840.4718-0.10410.03230.75280.05520.435823.30095.812329.2254
30.3027-0.1397-0.0180.44710.19381.25280.00420.00310.03820.0394-0.0501-0.061-0.03180.08620.05210.0995-0.01710.00260.10020.01990.1261-6.207718.720340.0815
44.80521.3971-0.24974.1025-0.77823.7638-0.12270.41150.2581-0.13540.0879-0.4352-0.34510.67870.02360.4348-0.06280.00250.88760.17680.595917.317825.698732.7812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:423)
2X-RAY DIFFRACTION2(chain A and resid 424:574)
3X-RAY DIFFRACTION3(chain B and resid 9:424)
4X-RAY DIFFRACTION4(chain B and resid 425:575)

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