PDB-4eq4: Crystal structure of seleno-methionine derivatized GH3.12

ID or keywords:

Entry

Database: PDB / ID: 4eq4

Title

Crystal structure of seleno-methionine derivatized GH3.12

Components

4-substituted benzoates-glutamate ligase GH3.12

Keywords

LIGASE / 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 / benzoate metabolic process / salicylic acid mediated signaling pathway / regulation of systemic acquired resistance / positive regulation of plant-type hypersensitive response / detection of fungus / plant-type hypersensitive response ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.074 Å

Authors

Zubieta, C. / Nanao, M. / Jez, J. / Westfall, C. / Kapp, U.

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 18, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 20, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 25, 2012	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4eq4.cif.gz	438.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4eq4.ent.gz	370.3 KB	Display	PDB format
PDBx/mmJSON format	4eq4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4eq4_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4eq4_full_validation.pdf.gz	1 MB	Display
Data in XML	4eq4_validation.xml.gz	48.6 KB	Display
Data in CIF	4eq4_validation.cif.gz	71 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eq/4eq4 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/4eq4	HTTPS FTP

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Related structure data

Related structure data	4eplC 4epmC 4eqlC 4ewvC C: citing same article (ref.)
Similar structure data	5kod-4 4l39-2 5kod-2 4b2g-2 5kod-1 4ewv-2 5cgt-d 4epl-d 4mq5-d 5kod-3 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	#117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #17 - May 2001 Cyclooxygenase 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: 4-substituted benzoates-glutamate ligase GH3.12

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

hetero molecules

134 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
67 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
67 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	90.865, 66.302, 100.451
Angle α, β, γ (deg.)	90.00, 106.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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: 66559.664 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-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆O₃
#3: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 663 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.05 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG 3350, 0.25M ammonium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2011 / Details: bent collimating mirror and toroid
Radiation	Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.08→60 Å / Num. obs: 134804 / % possible obs: 99.5 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 4.1 % / R_sym value: 0.252 / Net I/σ(I): 6.7
Reflection shell	Resolution: 2.08→2.2 Å / Redundancy: 4 % / R_merge(I) obs: 0.816 / Mean I/σ(I) obs: 1.9 / % possible all: 97.7

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.074→56.965 Å / SU ML: 0.26 / σ(F): 1.89 / Phase error: 25.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2524	6824	5.06 %
R_work	0.2141	-	-
obs	0.2161	69262	99.12 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 31.27 Å² / k_sol: 0.335 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.1657 Å²	0 Å²	6.7176 Å²
2-	-	-3.2452 Å²	0 Å²
3-	-	-	2.0795 Å²

Refinement step

Cycle: LAST / Resolution: 2.074→56.965 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8391	0	66	663	9120

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	8711
X-RAY DIFFRACTION	f_angle_d	1.347	11847
X-RAY DIFFRACTION	f_dihedral_angle_d	15.378	3201
X-RAY DIFFRACTION	f_chiral_restr	0.091	1341
X-RAY DIFFRACTION	f_plane_restr	0.005	1519

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 (%)
2.0745-2.098	0.3775	169	0.3121	3540	X-RAY DIFFRACTION	84
2.098-2.1227	0.3541	211	0.2812	4378	X-RAY DIFFRACTION	99
2.1227-2.1486	0.3059	218	0.2857	4279	X-RAY DIFFRACTION	100
2.1486-2.1758	0.3271	259	0.2856	4192	X-RAY DIFFRACTION	100
2.1758-2.2044	0.3001	205	0.2664	4447	X-RAY DIFFRACTION	100
2.2044-2.2346	0.3289	215	0.2614	4192	X-RAY DIFFRACTION	100
2.2346-2.2666	0.3337	202	0.2594	4327	X-RAY DIFFRACTION	99
2.2666-2.3004	0.2871	302	0.2506	4229	X-RAY DIFFRACTION	100
2.3004-2.3364	0.2748	213	0.253	4334	X-RAY DIFFRACTION	100
2.3364-2.3747	0.3252	255	0.2445	4271	X-RAY DIFFRACTION	100
2.3747-2.4156	0.3081	203	0.2443	4256	X-RAY DIFFRACTION	100
2.4156-2.4595	0.3151	238	0.2308	4333	X-RAY DIFFRACTION	100
2.4595-2.5068	0.3055	222	0.2374	4323	X-RAY DIFFRACTION	100
2.5068-2.558	0.2467	192	0.225	4321	X-RAY DIFFRACTION	100
2.558-2.6136	0.2919	199	0.2286	4344	X-RAY DIFFRACTION	100
2.6136-2.6744	0.2847	263	0.2256	4264	X-RAY DIFFRACTION	100
2.6744-2.7413	0.2665	230	0.2237	4279	X-RAY DIFFRACTION	100
2.7413-2.8154	0.2323	259	0.2131	4226	X-RAY DIFFRACTION	100
2.8154-2.8983	0.2712	227	0.2127	4269	X-RAY DIFFRACTION	100
2.8983-2.9918	0.2562	195	0.212	4348	X-RAY DIFFRACTION	100
2.9918-3.0987	0.2437	236	0.2048	4294	X-RAY DIFFRACTION	100
3.0987-3.2228	0.2527	230	0.2021	4297	X-RAY DIFFRACTION	100
3.2228-3.3695	0.2314	200	0.1905	4337	X-RAY DIFFRACTION	100
3.3695-3.5471	0.2238	237	0.1887	4243	X-RAY DIFFRACTION	99
3.5471-3.7693	0.2018	256	0.1799	4279	X-RAY DIFFRACTION	99
3.7693-4.0602	0.1928	252	0.1697	4235	X-RAY DIFFRACTION	99
4.0602-4.4687	0.1903	221	0.1635	4300	X-RAY DIFFRACTION	100
4.4687-5.1149	0.1941	237	0.1682	4287	X-RAY DIFFRACTION	100
5.1149-6.4429	0.2251	232	0.2264	4293	X-RAY DIFFRACTION	100
6.4429-56.9863	0.2638	246	0.2191	4263	X-RAY DIFFRACTION	99

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	0.8733	-0.0665	0.0468	0.208	0.0684	0.1988	0.0129	-0.0116	-0.0076	0.0463	-0.011	-0.0052	0.036	-0.0148	-0.0056	0.1036	-0.0076	-0.0067	0.0926	0.0099	0.0912	35.1209	13.1655	5.7964
2	1.0938	0.3082	-0.6299	0.1585	0.0212	1.13	0.0135	-0.5168	-0.4487	0.3594	-0.0769	0.0471	0.1854	0.0719	0.0277	0.6561	-0.0683	0.1237	0.767	0.0889	0.687	25.6751	1.1699	30.3084
3	0.2801	-0.076	-0.0238	0.3405	0.2698	1.2601	-0.0114	-0.001	0.0433	0.0747	-0.0435	-0.0283	0.022	0.0006	0.0484	0.1665	-0.0059	0.0199	0.1423	0.0116	0.1894	-6.3887	18.6404	39.6856
4	1.1955	0.243	-0.7711	0.3316	-0.156	0.7615	0.0731	0.1124	0.3139	-0.1324	0.2137	-0.3321	-0.3589	0.1713	-0.1944	0.5734	-0.0147	0.2402	0.7191	0.0706	0.8	20.302	29.0243	34.7189

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 9:417)
2	X-RAY DIFFRACTION	2	(chain A and resid 418:575)
3	X-RAY DIFFRACTION	3	(chain B and resid 9:418)
4	X-RAY DIFFRACTION	4	(chain B and resid 419:573)

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