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- PDB-6e1q: AtGH3.15 acyl acid amido synthetase in complex with 2,4-DB -

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Basic information

Entry
Database: PDB / ID: 6e1q
TitleAtGH3.15 acyl acid amido synthetase in complex with 2,4-DB
ComponentsAtGH3.15 acyl acid amido synthetase
KeywordsLIGASE / hormone modification / adenylating enzyme / acyl acid-amido synthetase / adenylation / plant protein
Function / homology
Function and homology information


auxin conjugate metabolic process / glutamine binding / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / ligase activity / ATP binding / cytosol
Similarity search - Function
: / : / GH3 family central domain / GH3 family C-terminal domain / GH3 family / GH3 family N-terminal domain
Similarity search - Domain/homology
(2,4-DICHLOROPHENOXY)ACETIC ACID / PHOSPHATE ION / Indole-3-acetic acid-amido synthetase GH3.15
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsSharp, A.M. / Lee, S.G. / Jez, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1614539 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Modification of auxinic phenoxyalkanoic acid herbicides by the acyl acid amido synthetase GH3.15 from Arabidopsis.
Authors: Sherp, A.M. / Lee, S.G. / Schraft, E. / Jez, J.M.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AtGH3.15 acyl acid amido synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5904
Polymers67,0521
Non-polymers5373
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-30 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.798, 154.789, 73.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-174-

ASN

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Components

#1: Protein AtGH3.15 acyl acid amido synthetase / Auxin-responsive GH3 family protein / Putative auxin responsive protein / At5g13370


Mass: 67052.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g13370, At5g13370/T22N19_20, T22N19.20, T22N19_20 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8GZ29, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CFA / (2,4-DICHLOROPHENOXY)ACETIC ACID / 2,4-DICHLOROPHENOXYACETIC ACID


Mass: 221.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6Cl2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.2 M potassium phosphate dibasic, 0.8 M sodium phosphate monobasic, 0.1 M sodium acetate/acetic acid, 2.5 mM 2,4-DB

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.148→38.7 Å / Num. obs: 47900 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.047 / Net I/σ(I): 18.5
Reflection shellResolution: 2.148→2.19 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.557 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6AVH

6avh


Resolution: 2.148→38.697 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 2000 4.18 %
Rwork0.182 --
obs0.1833 47873 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.148→38.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4491 0 31 288 4810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074683
X-RAY DIFFRACTIONf_angle_d0.9196363
X-RAY DIFFRACTIONf_dihedral_angle_d2.5724999
X-RAY DIFFRACTIONf_chiral_restr0.055724
X-RAY DIFFRACTIONf_plane_restr0.006810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1481-2.20190.24761420.23143183X-RAY DIFFRACTION98
2.2019-2.26140.27091390.22323243X-RAY DIFFRACTION100
2.2614-2.32790.26421400.22193226X-RAY DIFFRACTION100
2.3279-2.40310.24391430.22023241X-RAY DIFFRACTION99
2.4031-2.48890.26151410.21623263X-RAY DIFFRACTION100
2.4889-2.58860.25941400.20753268X-RAY DIFFRACTION100
2.5886-2.70630.22751470.21083258X-RAY DIFFRACTION100
2.7063-2.8490.24741400.20193236X-RAY DIFFRACTION99
2.849-3.02740.22291420.20083271X-RAY DIFFRACTION100
3.0274-3.26110.24241420.19373289X-RAY DIFFRACTION100
3.2611-3.5890.20071440.17773303X-RAY DIFFRACTION100
3.589-4.10780.21281480.15853295X-RAY DIFFRACTION99
4.1078-5.17350.16191480.14383345X-RAY DIFFRACTION100
5.1735-38.70350.19841440.1763452X-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)
10.78150.63640.2625.8621.81731.76370.1799-0.2236-0.16940.7393-0.1292-0.30490.32830.1224-0.03780.3228-0.0321-0.04570.32640.02410.319925.1533-66.489818.8904
21.233-0.13840.58910.6794-0.18991.3274-0.0263-0.1134-0.03010.06250.0314-0.0027-0.1234-0.1127-0.00640.2388-0.01720.01620.2475-0.0320.21713.6802-50.68084.0514
33.52282.9113-1.34753.6926-1.57542.4297-0.61990.4934-0.3685-0.70830.3492-0.5120.3817-0.01190.14120.3626-0.07490.06620.2769-0.01020.378732.5313-50.5611-17.154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 427 )
3X-RAY DIFFRACTION3chain 'A' and (resid 428 through 587 )

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