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- PDB-7vka: Crystal Structure of GH3.6 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 7vka
TitleCrystal Structure of GH3.6 in complex with an inhibitor
ComponentsIndole-3-acetic acid-amido synthetase GH3.6
KeywordsLIGASE / Inhibitor / Complex
Function / homology
Function and homology information


indole-3-acetic acid amido synthetase activity / unidimensional cell growth / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / response to auxin / auxin-activated signaling pathway / 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-7IS / ADENOSINE MONOPHOSPHATE / Indole-3-acetic acid-amido synthetase GH3.6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsWang, N. / Luo, M. / Bao, H. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentKQTD20190929173906742 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Chemical genetic screening identifies nalacin as an inhibitor of GH3 amido synthetase for auxin conjugation.
Authors: Xie, Y. / Zhu, Y. / Wang, N. / Luo, M. / Ota, T. / Guo, R. / Takahashi, I. / Yu, Z. / Aizezi, Y. / Zhang, L. / Yan, Y. / Zhang, Y. / Bao, H. / Wang, Y. / Zhu, Z. / Huang, A.C. / Zhao, Y. / ...Authors: Xie, Y. / Zhu, Y. / Wang, N. / Luo, M. / Ota, T. / Guo, R. / Takahashi, I. / Yu, Z. / Aizezi, Y. / Zhang, L. / Yan, Y. / Zhang, Y. / Bao, H. / Wang, Y. / Zhu, Z. / Huang, A.C. / Zhao, Y. / Asami, T. / Huang, H. / Guo, H. / Jiang, K.
History
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Indole-3-acetic acid-amido synthetase GH3.6
B: Indole-3-acetic acid-amido synthetase GH3.6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,6877
Polymers138,1152
Non-polymers1,5725
Water7,873437
1
A: Indole-3-acetic acid-amido synthetase GH3.6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8894
Polymers69,0571
Non-polymers8323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-4 kcal/mol
Surface area24670 Å2
MethodPISA
2
B: Indole-3-acetic acid-amido synthetase GH3.6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7973
Polymers69,0571
Non-polymers7402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-3 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.871, 205.871, 65.665
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Indole-3-acetic acid-amido synthetase GH3.6 / Auxin-responsive GH3-like protein 6 / AtGH3-6 / Protein DWARF IN LIGHT 1 / DFL-1


Mass: 69057.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GH3.6, DFL1, At5g54510, F24B18.13 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LSQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-7IS / N-[4-[(6-chloranylpyridazin-3-yl)amino]phenyl]-3-(trifluoromethyl)benzamide


Mass: 392.762 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H12ClF3N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride, 0.1M Tris pH 8.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 62068 / % possible obs: 99.4 % / Redundancy: 11 % / Biso Wilson estimate: 30.45 Å2 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.052 / Rrim(I) all: 0.192 / Χ2: 0.465 / Net I/σ(I): 2.6 / Num. measured all: 682118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4940.45759510.3310.2360.5180.26496.4
2.49-2.596.50.46161590.510.1840.4990.28499.6
2.59-2.78.40.46161930.5930.1610.490.33199.8
2.7-2.859.40.40262200.8250.1310.4240.32499.8
2.85-3.0211.10.35161860.9160.1030.3670.35899.9
3.02-3.26120.29362160.9550.0830.3050.41599.9
3.26-3.5812.60.23162250.980.0650.2410.51499.8
3.58-4.114.60.17562300.9910.0450.1810.61499.9
4.1-5.1715.20.12362910.9950.0310.1270.59699.8
5.17-4015.60.09663970.9970.0240.0990.52399.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KOD

5kod


Resolution: 2.401→35.658 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 3051 4.93 %
Rwork0.1717 58859 -
obs0.1752 61910 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.48 Å2 / Biso mean: 38.4613 Å2 / Biso min: 6.92 Å2
Refinement stepCycle: final / Resolution: 2.401→35.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9387 0 106 438 9931
Biso mean--48.5 35.55 -
Num. residues----1184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.401-2.43820.33051330.2842246692
2.4382-2.47820.36441340.2807259698
2.4782-2.52090.34491640.2534264999
2.5209-2.56670.34281550.2452643100
2.5667-2.61610.29371340.23192671100
2.6161-2.66940.34481340.22382685100
2.6694-2.72750.28991340.21332678100
2.7275-2.79090.26481360.20322685100
2.7909-2.86060.30731470.20292662100
2.8606-2.9380.28561460.19882690100
2.938-3.02440.28151230.18912700100
3.0244-3.12190.26231180.17922713100
3.1219-3.23340.23941540.17732667100
3.2334-3.36280.26311350.17222686100
3.3628-3.51570.2641410.16972690100
3.5157-3.70090.24811090.1562731100
3.7009-3.93250.2131370.14332713100
3.9325-4.23570.19641480.12922677100
4.2357-4.66110.171260.1222738100
4.6611-5.33370.1851300.11912722100
5.3337-6.71250.19681600.15612730100
6.7125-35.6580.19151530.1485266795
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)
11.08030.82180.40511.29640.4780.72370.0449-0.0151-0.10710.1286-0.0039-0.13770.12620.0578-0.03430.2020.0359-0.0260.27270.00250.2094-35.989737.199327.8824
20.4009-0.0760.85890.45690.77523.6914-0.11030.01960.1745-0.10160.002-0.0517-0.3581-0.00470.11250.1954-0.0201-0.0150.2029-0.00080.281-37.516857.671621.173
31.4842-1.1518-0.3012.70070.59782.64890.08870.2075-0.0782-0.2697-0.07180.09020.05570.00880.01010.2022-0.03450.00470.2404-0.0320.1911-50.369848.44270.9907
41.7050.6501-0.29391.0744-0.1861.8740.02950.0328-0.1743-0.0159-0.04170.02940.4351-0.02560.00470.34570.00810.0020.197-0.02510.2156-17.480890.0052-8.4836
50.86430.0220.32740.48780.5487.17410.0832-0.04210.06120.0171-0.00850.02020.3558-0.4578-0.05750.1678-0.00910.00430.2110.04530.2151-28.9298.89779.5109
63.51-1.69610.48342.1574-0.86842.5373-0.0131-0.1716-0.11010.06990.00410.11630.15830.04530.05690.2047-0.0254-0.01340.1977-0.00380.189-26.3722103.710618.1446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 354 )A13 - 354
2X-RAY DIFFRACTION2chain 'A' and (resid 355 through 477 )A355 - 477
3X-RAY DIFFRACTION3chain 'A' and (resid 478 through 609 )A478 - 609
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 426 )B13 - 426
5X-RAY DIFFRACTION5chain 'B' and (resid 427 through 503 )B427 - 503
6X-RAY DIFFRACTION6chain 'B' and (resid 504 through 609 )B504 - 609

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