PDB-4ewv: Crystal structure of GH3.12 in complex with AMPCPP

ID or keywords:

Entry

Database: PDB / ID: 4ewv

Title

Crystal structure of GH3.12 in complex with AMPCPP

Components

4-substituted benzoates-glutamate ligase GH3.12

Keywords

LIGASE / firefly luciferase family / adenylation / amino acid conjugation

Function / homology

Function and homology information

N-(4-aminobenzoyl)-L-glutamate synthetase activity / N-benzoyl-L-glutamate synthetase activity / N-vanillate-L-glutamate synthetase activity / N-(4-hydroxybenzoyl)-L-glutamate synthetase activity / positive regulation of plant-type hypersensitive response / benzoate metabolic process / salicylic acid mediated signaling pathway / regulation of systemic acquired resistance / detection of fungus / plant-type hypersensitive response ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.897 Å

Authors

Zubieta, C. / Nanao, M. / Jez, J.

Citation

Journal: 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

Deposition	Apr 28, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 25, 2012	Group: Database references
Revision 1.2	Sep 13, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ewv.cif.gz	384 KB	Display	PDBx/mmCIF format
PDB format	pdb4ewv.ent.gz	312.5 KB	Display	PDB format
PDBx/mmJSON format	4ewv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ewv_validation.pdf.gz	999.4 KB	Display	wwPDB validaton report
Full document	4ewv_full_validation.pdf.gz	1 MB	Display
Data in XML	4ewv_validation.xml.gz	36.4 KB	Display
Data in CIF	4ewv_validation.cif.gz	48.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ew/4ewv ftp://data.pdbj.org/pub/pdb/validation_reports/ew/4ewv	HTTPS FTP

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Related structure data

Related structure data	4eplC 4epmC 4eq4C 4eqlSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6avh-2 5mqp-2 4olh-1 4olh-2 5i7h-1 6j1g-d 6j1h-1 4msu-1 5mqp-4 5tj7-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#104 - Aug 2008 Selenocysteine Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #251 - Nov 2020 Adenylyl Cyclase similarity (1)

Deposited unit

A: 4-substituted benzoates-glutamate ligase GH3.12

B: 4-substituted benzoates-glutamate ligase GH3.12

hetero molecules

133 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 4-substituted benzoates-glutamate ligase GH3.12

hetero molecules

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

2

B: 4-substituted benzoates-glutamate ligase GH3.12

hetero molecules

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

Unit cell

Length a, b, c (Å)	116.348, 116.348, 94.663
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 49.94 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 1.8M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2011
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection twin	Operator: h,-k,-l / Fraction: 0.502
Reflection	Resolution: 2.9→52 Å / Num. all: 28232 / Num. obs: 27316 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / R_merge(I) obs: 0.098 / R_sym value: 0.098 / Net I/σ(I): 13.7
Reflection shell	Resolution: 2.9→2.98 Å / Redundancy: 4 % / R_merge(I) obs: 0.72 / Mean I/σ(I) obs: 2.1 / R_sym value: 0.021 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4EQL

4eql

Resolution: 2.897→52.032 Å / σ(F): 1.35 / Phase error: 29.57 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2859	1368	5.01 %
R_work	0.2434	-	-
obs	0.2457	27316	96.76 %
all	-	28232	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 121.767 Å² / k_sol: 0.329 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.0077 Å²	-0 Å²	-0 Å²
2-	-	-0.0077 Å²	-0 Å²
3-	-	-	0.0155 Å²

Refinement step

Cycle: LAST / Resolution: 2.897→52.032 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7098	0	63	0	7161

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7310
X-RAY DIFFRACTION	f_angle_d	0.849	9970
X-RAY DIFFRACTION	f_dihedral_angle_d	12.717	2451
X-RAY DIFFRACTION	f_chiral_restr	0.063	1178
X-RAY DIFFRACTION	f_plane_restr	0.003	1262

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 (%)
2.9003-3.0037	0.3748	145	0.2958	2649	X-RAY DIFFRACTION	95
3.0037-3.1238	0.3449	126	0.29	2654	X-RAY DIFFRACTION	95
3.1238-3.2656	0.3302	131	0.2792	2674	X-RAY DIFFRACTION	95
3.2656-3.4374	0.3078	117	0.2771	2673	X-RAY DIFFRACTION	96
3.4374-3.6521	0.3114	134	0.2608	2364	X-RAY DIFFRACTION	84
3.6521-3.933	0.304	112	0.2546	2142	X-RAY DIFFRACTION	77
3.933-4.3268	0.2693	156	0.2422	2665	X-RAY DIFFRACTION	94
4.3268-4.9484	0.2412	150	0.2219	2646	X-RAY DIFFRACTION	94
4.9484-6.2175	0.3221	154	0.242	2669	X-RAY DIFFRACTION	95
6.2175-24.4772	0.2418	142	0.2038	2719	X-RAY DIFFRACTION	95

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	1.9026	0.2009	-2.3391	0.0385	-0.2403	2.8777	-0.08	0.6649	-0.4038	-0.0909	0.117	0.1788	0.1841	-0.3155	0.0154	0.6834	-0.0575	0.1725	1.0244	-0.4986	1.3963	7.6165	-37.5579	-0.518
2	3.8699	-0.7375	2.3599	2.1684	-0.6898	2.4323	-0.3661	-0.6754	0.5162	0.4743	0.012	-0.5928	-0.2304	0.5121	0.3749	0.2855	0.1344	-0.1649	0.4724	0.0183	0.4777	11.1872	-30.9372	-12.2343
3	0.8913	-0.4302	-0.7086	0.3836	0.1605	0.7337	0.1554	0.0268	0.2962	-0.0931	0.0404	-0.0441	-0.3272	-0.0508	-0.0234	0.2997	0.0557	-0.0904	0.0308	-0.0151	0.234	33.3613	-25.4584	-3.8669
4	0.3971	-0.3559	-0.6183	2.704	-1.5134	3.0493	0.207	-0.2133	-0.2834	0.5366	-0.5576	-1.3342	0.5629	0.8404	0.4446	0.2957	0.0079	-0.0872	0.2671	0.1923	0.5977	50.9948	-19.4501	-8.364
5	2.4613	-1.0429	0.484	0.4524	-0.167	0.2431	-0.0761	-0.1396	0.3717	0.1198	0.0876	-0.139	-0.1057	-0.0206	0.0013	0.3876	0.3185	-0.0083	0.2716	-0.0032	0.1968	33.8227	-35.4099	6.7981
6	8.0215	-4.1043	0.696	3.9376	-1.2117	3.2839	-0.1834	-0.1346	0.7389	0.0843	0.0673	-0.5333	0.0081	0.3048	0.0565	0.3155	0.1358	0.1729	0.3438	0.1752	0.9404	17.3315	-45.7517	6.0027
7	3.0345	-0.353	-0.6908	3.3939	-0.5873	1.9637	-0.0216	0.1565	-0.2372	-0.1407	0.0829	-0.0632	0.1681	-0.0725	0.0319	-0.0624	0.0156	-0.0915	-0.1549	-0.0326	0.0797	43.2494	-57.3983	-1.3399
8	0.1838	-0.1411	0.1501	0.7832	-0.142	0.3207	0.0452	-0.0758	0.0144	-0.0253	0.0078	0.0472	0.0754	-0.105	-0.0608	-0.0424	-0.2659	-0.0116	-0.049	0.055	0.102	40.8965	-54.2284	-9.4137
9	0.3457	0.1969	0.2002	0.3259	0.0303	0.1487	-0.0658	-0.1401	0.107	0.235	0.1228	0.0832	-0.1168	-0.1484	-0.076	0.4564	0.1655	0.231	0.2814	-0.054	0.6532	20.1358	-52.1001	-48.2583
10	0.2963	0.2324	0.0415	1.0365	-0.4648	0.2961	-0.0313	-0.0145	-0.3447	-0.0017	0.0071	0.0403	0.2806	-0.0536	0.0512	0.4514	0.0663	0.0115	0.0954	-0.0313	0.4825	25.642	-48.7508	-38.0586
11	1.7764	0.3331	0.2965	1.8692	-1.1787	0.9815	0.0034	0.2084	-0.1369	-0.0574	-0.0731	-0.1855	0.068	0.1561	0.0468	0.1815	0.2557	-0.0363	0.268	0.0551	0.1767	32.9922	-24.2195	-46.288
12	2.6703	1.5161	-1.7053	1.6661	-1.2048	2.096	0.0402	-0.532	-0.6371	0.0328	-0.3726	-0.5347	0.1295	0.7041	0.3348	0.2519	-0.1699	0.1414	0.5192	0.0181	0.5641	38.7902	-7.1391	-40.9356
13	5.9818	0.4308	-2.6246	1.5378	-0.1416	3.4582	0.3985	0.2636	0.6034	-0.2717	-0.3123	-0.3212	-0.2736	0.2718	-0.0066	0.1822	0.193	0.0804	0.3741	0.1577	0.209	23.8375	-19.3337	-54.999
14	0.4103	0.1526	0.0439	1.3967	-0.3775	0.5075	-0.0098	-0.1022	-0.2335	0.1632	0.0219	-0.0917	0.1579	0.1006	-0.0163	0.2079	0.1711	-0.0268	0.1207	0.06	0.3083	15.5109	-38.4468	-57.3436
15	0.3443	-0.0054	-0.4797	1.4005	-0.5754	1.9443	0.0594	-0.0321	0.0563	-0.0523	-0.1196	-0.5806	-0.1273	0.2887	0.0746	0.0471	0.0024	-0.0612	0.0241	0.0703	0.3538	0.9144	-15.8859	-47.9494
16	2.9355	1.3548	0.0093	4.4889	1.2661	4.2276	-0.0157	-0.3082	-0.3424	0.1468	-0.0694	-0.1125	0.5421	0.2207	-0.0145	0.264	-0.0329	-0.0342	0.063	0.1144	0.2742	3.333	-17.2371	-39.8101

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 8:79)
2	X-RAY DIFFRACTION	2	(chain A and resid 80:115)
3	X-RAY DIFFRACTION	3	(chain A and resid 116:233)
4	X-RAY DIFFRACTION	4	(chain A and resid 234:283)
5	X-RAY DIFFRACTION	5	(chain A and resid 284:353)
6	X-RAY DIFFRACTION	6	(chain A and resid 354:419)
7	X-RAY DIFFRACTION	7	(chain A and resid 420:506)
8	X-RAY DIFFRACTION	8	(chain A and resid 507:601)
9	X-RAY DIFFRACTION	9	(chain B and resid 8:79)
10	X-RAY DIFFRACTION	10	(chain B and resid 80:115)
11	X-RAY DIFFRACTION	11	(chain B and resid 116:234)
12	X-RAY DIFFRACTION	12	(chain B and resid 235:283)
13	X-RAY DIFFRACTION	13	(chain B and resid 284:330)
14	X-RAY DIFFRACTION	14	(chain B and resid 331:416)
15	X-RAY DIFFRACTION	15	(chain B and resid 417:506)
16	X-RAY DIFFRACTION	16	(chain B and resid 507:601)

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