PDB-6avh: GH3.15 acyl acid amido synthetase

ID or keywords:

Entry

Database: PDB / ID: 6avh

Title

GH3.15 acyl acid amido synthetase

Components

GH3.15 acyl acid amido synthetase

Keywords

LIGASE / PLANT PROTEIN / auxin / plant hormone / amino acid

Function / homology

Function and homology information

auxin conjugate metabolic process / glutamine binding / acid-amino acid ligase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / ATP binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.011 Å

Authors

Sherp, A.M. / Jez, J.M.

Funding support

United States, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Arabidopsis thalianaGH3.15 acyl acid amido synthetase has a highly specific substrate preference for the auxin precursor indole-3-butyric acid.
Authors: Sherp, A.M. / Westfall, C.S. / Alvarez, S. / Jez, J.M.

History

Deposition	Sep 2, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Apr 4, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6avh.cif.gz	866.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6avh.ent.gz	723.8 KB	Display	PDB format
PDBx/mmJSON format	6avh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6avh_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	6avh_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6avh_validation.xml.gz	78.6 KB	Display
Data in CIF	6avh_validation.cif.gz	105.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/av/6avh ftp://data.pdbj.org/pub/pdb/validation_reports/av/6avh	HTTPS FTP

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Related structure data

Related structure data	4eplS S: Starting model for refinement
Similar structure data	6eeq-d 6xd1-d 5mqp-3 4ewv-2 6j6x-d 5mqp-7 4gm1-d 6dns-d 5mqp-1 1e6e-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4eplS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: GH3.15 acyl acid amido synthetase

B: GH3.15 acyl acid amido synthetase

C: GH3.15 acyl acid amido synthetase

D: GH3.15 acyl acid amido synthetase

hetero molecules

270 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GH3.15 acyl acid amido synthetase

hetero molecules

defined by author
Evidence: gel filtration
67.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: GH3.15 acyl acid amido synthetase

hetero molecules

defined by author
67.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: GH3.15 acyl acid amido synthetase

hetero molecules

defined by author
67.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: GH3.15 acyl acid amido synthetase

hetero molecules

defined by author
67.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	180.911, 191.605, 319.364
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	22
Space group name H-M	F222

Components on special symmetry positions

ID	Model	Components
1	1	D-276- GLN

#1: Protein	GH3.15 acyl acid amido synthetase / At5g13370 / Auxin-responsive GH3 family protein / Putative auxin responsive protein Mass: 67052.461 Da / Num. of mol.: 4 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 (E. coli) / References: UniProt: Q8GZ29, Ligases
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM

#1: Protein

GH3.15 acyl acid amido synthetase / At5g13370 / Auxin-responsive GH3 family protein / Putative auxin responsive protein

Mass: 67052.461 Da / Num. of mol.: 4
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 (E. coli) / References: UniProt: Q8GZ29, Ligases

#2: Chemical

ChemComp-AMP / ADENOSINE MONOPHOSPHATE

Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.32 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 25% PEG1500, 0.1 M MIB (sodium malonate, imidazole, boric acid), pH 5.0, 2 mM AMP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 3.011→159.682 Å / Num. obs: 54417 / % possible obs: 100 % / Redundancy: 7.4 % / R_sym value: 0.117 / Net I/σ(I): 14.9
Reflection shell	Resolution: 3.011→3.09 Å / Mean I/σ(I) obs: 2.6 / R_sym value: 0.759 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4EPL

4epl

Resolution: 3.011→46.528 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.07

	R_factor	Num. reflection	% reflection
R_free	0.2494	1995	3.67 %
R_work	0.1851	-	-
obs	0.1875	54296	99.14 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.011→46.528 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17307	0	92	0	17399

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	17771
X-RAY DIFFRACTION	f_angle_d	1.405	24094
X-RAY DIFFRACTION	f_dihedral_angle_d	4.041	10724
X-RAY DIFFRACTION	f_chiral_restr	0.073	2762
X-RAY DIFFRACTION	f_plane_restr	0.009	3034

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.0106-3.0858	0.3628	140	0.2455	3364	X-RAY DIFFRACTION	91
3.0858-3.1693	0.2894	133	0.2326	3743	X-RAY DIFFRACTION	100
3.1693-3.2625	0.3258	144	0.2228	3729	X-RAY DIFFRACTION	100
3.2625-3.3678	0.292	146	0.2088	3738	X-RAY DIFFRACTION	100
3.3678-3.4881	0.3225	140	0.2063	3743	X-RAY DIFFRACTION	100
3.4881-3.6277	0.248	141	0.1984	3742	X-RAY DIFFRACTION	100
3.6277-3.7927	0.2833	141	0.1912	3771	X-RAY DIFFRACTION	100
3.7927-3.9926	0.2848	149	0.1842	3758	X-RAY DIFFRACTION	100
3.9926-4.2426	0.2296	133	0.1633	3748	X-RAY DIFFRACTION	100
4.2426-4.5699	0.1969	143	0.1509	3790	X-RAY DIFFRACTION	100
4.5699-5.0293	0.2033	139	0.1519	3754	X-RAY DIFFRACTION	100
5.0293-5.7559	0.2396	155	0.1703	3792	X-RAY DIFFRACTION	100
5.7559-7.2474	0.2521	142	0.1953	3809	X-RAY DIFFRACTION	100
7.2474-46.5338	0.193	149	0.1856	3820	X-RAY DIFFRACTION	97

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.5906	-0.1818	-1.199	2.5719	-0.1182	2.4863	0.1464	-0.1499	-0.6391	-0.1372	-0.3226	0.218	0.2154	-0.0055	0.1615	0.2676	-0.0349	-0.0845	0.3313	0.0686	0.4659	-69.3643	-51.7566	25.0719
2	1.5995	0.9686	-0.4221	2.3134	-0.9572	2.098	-0.0558	0.2254	0.1862	-0.2898	0.1123	0.2204	-0.175	-0.1364	-0.0433	0.2892	0.0569	-0.0483	0.384	0.0075	0.3957	-65.1913	-27.0946	13.9119
3	3.7128	2.0037	0.9488	2.2194	0.8269	0.6498	0.0278	-0.2411	0.1718	-0.0101	0.0416	0.1183	-0.084	-0.0938	0.0091	0.2768	0.0397	0.0326	0.3202	0.0007	0.3256	-55.7527	-23.8158	35.0933
4	3.1605	0.6415	2.2859	0.7229	-0.2851	4.9112	0.0134	0.004	-0.0044	-0.0382	0.0612	-0.1454	-0.0011	0.2552	-0.0478	0.2406	0.0528	0.0296	0.2436	-0.0281	0.4112	-46.1361	-19.9641	33.6273
5	5.7114	1.7493	-0.133	3.6041	0.4008	2.0736	-0.0352	0.487	-0.7224	-0.1312	-0.0822	-0.6418	0.3142	0.3021	0.0155	0.3569	0.1313	-0.0341	0.4459	-0.0317	0.6641	-63.6042	-5.3411	54.0379
6	5.6257	1.9692	1.2864	4.7719	2.8472	3.147	0.2126	0.2545	-0.2864	0.0582	0.0831	-0.933	-0.0331	0.3839	-0.2179	0.3498	-0.0782	-0.0401	0.4485	0.0319	0.4713	-65.6133	6.1801	66.1769
7	1.7822	-0.7788	-0.7623	2.6771	1.0279	2.3721	0.1242	-0.1366	0.1961	0.232	0.0942	-0.3303	-0.2125	0.172	-0.2101	0.3253	-0.0447	-0.0177	0.3705	-0.0301	0.4784	-69.7342	19.6548	65.6845
8	3.2932	-1.3965	1.4897	3.9926	-1.5573	4.132	0.1728	0.3479	0.0871	-0.3406	-0.0011	0.1333	0.0592	0.0287	-0.1253	0.3726	0.0008	0.0499	0.3773	0.071	0.4202	-84.9924	29.2142	43.7651
9	2.7668	-1.1456	0.8596	1.2202	-0.2922	3.6864	-0.028	-0.3285	-0.2434	0.0931	0.3562	0.2281	0.1303	-0.5506	-0.6097	0.3385	-0.0729	0.0524	0.4205	0.1115	0.5265	-88.6912	23.4293	53.6582
10	3.89	-1.5509	-0.2884	2.7881	0.7162	2.7486	0.1193	0.161	0.2601	-0.166	-0.1574	-0.3466	-0.2471	0.1871	0.0593	0.3621	-0.0148	0.0097	0.3067	0.0891	0.3263	-22.0989	45.9908	20.0958
11	1.7816	0.0848	0.2965	2.0551	0.6692	2.4352	-0.0052	0.8201	-0.4036	-0.3914	0.1406	-0.206	0.478	-0.1047	-0.1624	0.5798	-0.0962	-0.0477	0.6775	-0.2178	0.5484	-32.6395	22.9897	1.5597
12	1.8392	0.831	-0.5994	1.1558	-0.6375	1.2572	0.053	0.0405	-0.2482	-0.0083	0.0407	0.0604	0.1766	0.0204	-0.1063	0.3115	0.0611	-0.0643	0.3468	0.0119	0.4927	-33.2211	24.5497	30.3916
13	2.8648	0.2156	0.4335	1.2855	-0.3137	2.0929	0.0968	-0.1768	0.0969	0.1153	-0.2341	0.0773	-0.0445	-0.215	0.1504	0.3122	-0.0087	0.0267	0.3206	-0.082	0.3226	-20.7245	-4.726	61.9613
14	2.1369	-0.4703	1.212	1.2585	-0.2604	2.2419	0.1612	-0.3068	-0.3781	0.2046	0.0598	0.034	0.3864	-0.2359	-0.2474	0.3377	-0.0555	-0.0108	0.3392	0.0222	0.3824	-17.7903	-23.0946	64.4913
15	2.155	-0.2237	-0.9112	1.7939	0.2214	4.571	-0.1066	0.0419	-0.4411	0.069	0.0039	-0.1777	0.3063	-0.0622	0.1161	0.2213	-0.0271	0.0163	0.2846	0.0021	0.4964	-1.6199	-29.3415	45.1862

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 111 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 112 through 407 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 408 through 486 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 487 through 586 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 7 through 78 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 79 through 144 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 145 through 426 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 427 through 536 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 537 through 586 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 3 through 144 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 145 through 295 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 296 through 587 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 3 through 193 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 194 through 427 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 428 through 588 )

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