PDB-6dhv: Structure of Arabidopsis Fatty Acid Amide Hydrolase

ID or keywords:

Entry

Database: PDB / ID: 6dhv

Title

Structure of Arabidopsis Fatty Acid Amide Hydrolase

Components

Fatty acid amide hydrolase

Keywords

HYDROLASE / FAAH / NAE signaling

Function / homology

Function and homology information

N-(long-chain-acyl)ethanolamine deacylase activity / N-acylethanolamine metabolic process / fatty acid amide hydrolase / fatty acid amide hydrolase activity / plant-type vacuole / plastid / lipid catabolic process / defense response to bacterium / endoplasmic reticulum membrane / Golgi apparatus ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.099 Å

Authors

Aziz, M. / Wang, X. / Tripathi, A. / Bankaitis, V. / Chapman, K.D.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2019
Title: Structural analysis of a plant fatty acid amide hydrolase provides insights into the evolutionary diversity of bioactive acylethanolamides.
Authors: Aziz, M. / Wang, X. / Tripathi, A. / Bankaitis, V.A. / Chapman, K.D.

History

Deposition	May 21, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	May 15, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _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 11, 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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PDBx/mmCIF format	6dhv.cif.gz	471.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6dhv.ent.gz	390.9 KB	Display	PDB format
PDBx/mmJSON format	6dhv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6dhv_validation.pdf.gz	439.6 KB	Display	wwPDB validaton report
Full document	6dhv_full_validation.pdf.gz	452.4 KB	Display
Data in XML	6dhv_validation.xml.gz	44.6 KB	Display
Data in CIF	6dhv_validation.cif.gz	63.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/6dhv ftp://data.pdbj.org/pub/pdb/validation_reports/dh/6dhv	HTTPS FTP

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Related structure data

Related structure data	6diiC 3kfuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6dii-2 3l2e-1 3l2e-2 1som-1 5ux5-2 5ux5-4 4mmd-d 3l2d-1 3l2d-2 3jpz-d 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

Deposited unit

A: Fatty acid amide hydrolase

B: Fatty acid amide hydrolase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	72.083, 79.660, 132.592
Angle α, β, γ (deg.)	90.00, 104.44, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fatty acid amide hydrolase / N-acylethanolamine amidohydrolase Mass: 69579.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FAAH, At5g64440, T12B11.3 / Plasmid: pTrcHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q7XJJ7, fatty acid amide hydrolase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Fatty acid amide hydrolase / N-acylethanolamine amidohydrolase

Mass: 69579.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: FAAH, At5g64440, T12B11.3 / Plasmid: pTrcHis2 / Production host:

Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q7XJJ7, fatty acid amide hydrolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.83 Å³/Da / Density % sol: 56.54 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, pH 6.0, 30% PEG 200, 5% PEG 3350

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Data collection

Diffraction

Mean temperature: 93.15 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL14-1 / Wavelength: 1.1808 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1808 Å / Relative weight: 1

Reflection

Resolution: 2.1→100 Å / Num. obs: 83848 / % possible obs: 98.9 % / Redundancy: 3.4 % / B_iso Wilson estimate: 45.35 Å² / R_merge(I) obs: 0.061 / R_pim(I) all: 0.038 / R_rim(I) all: 0.072 / Χ²: 1.07 / Net I/σ(I): 11.9 / Num. measured all: 282744

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.1-2.18	3	0.633	7761	0.773	0.403	0.753	1.076	91.9
2.18-2.26	3.2	0.489	8269	0.85	0.31	0.581	1.095	98.8
2.26-2.37	3.4	0.366	8441	0.917	0.229	0.433	1.093	100
2.37-2.49	3.4	0.272	8475	0.95	0.169	0.321	1.097	100
2.49-2.65	3.5	0.207	8414	0.968	0.128	0.244	1.079	100
2.65-2.85	3.5	0.144	8451	0.981	0.089	0.169	1.089	100
2.85-3.14	3.5	0.099	8455	0.99	0.061	0.117	1.022	100
3.14-3.59	3.4	0.07	8508	0.992	0.044	0.083	1.085	99.8
3.59-4.52	3.4	0.052	8457	0.994	0.033	0.062	1.024	99.9
4.52-100	3.4	0.034	8617	0.998	0.021	0.041	1.046	99.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KFU

3kfu

Resolution: 2.099→33.004 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2196	4315	5.15 %
R_work	0.1915	-	-
obs	0.193	83783	98.49 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.099→33.004 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9119	0	0	418	9537

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9311
X-RAY DIFFRACTION	f_angle_d	0.625	12640
X-RAY DIFFRACTION	f_dihedral_angle_d	11.811	5662
X-RAY DIFFRACTION	f_chiral_restr	0.043	1450
X-RAY DIFFRACTION	f_plane_restr	0.004	1629

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 (%)
2.0993-2.1231	0.3811	81	0.3332	2014	X-RAY DIFFRACTION	75
2.1231-2.1481	0.3311	147	0.3413	2454	X-RAY DIFFRACTION	92
2.1481-2.1743	0.3512	105	0.3155	2578	X-RAY DIFFRACTION	95
2.1743-2.2018	0.2865	139	0.2972	2608	X-RAY DIFFRACTION	97
2.2018-2.2308	0.3204	143	0.2952	2657	X-RAY DIFFRACTION	99
2.2308-2.2613	0.3016	133	0.2827	2672	X-RAY DIFFRACTION	100
2.2613-2.2936	0.3137	138	0.2806	2662	X-RAY DIFFRACTION	100
2.2936-2.3278	0.2838	160	0.2611	2717	X-RAY DIFFRACTION	100
2.3278-2.3642	0.2587	140	0.2285	2612	X-RAY DIFFRACTION	100
2.3642-2.403	0.2553	151	0.2371	2730	X-RAY DIFFRACTION	100
2.403-2.4444	0.2558	132	0.2206	2657	X-RAY DIFFRACTION	100
2.4444-2.4888	0.2363	144	0.2171	2697	X-RAY DIFFRACTION	100
2.4888-2.5367	0.2609	151	0.2237	2649	X-RAY DIFFRACTION	100
2.5367-2.5884	0.2746	157	0.2138	2670	X-RAY DIFFRACTION	100
2.5884-2.6447	0.277	139	0.2125	2678	X-RAY DIFFRACTION	100
2.6447-2.7062	0.2907	163	0.2079	2674	X-RAY DIFFRACTION	100
2.7062-2.7738	0.2172	136	0.214	2723	X-RAY DIFFRACTION	100
2.7738-2.8488	0.2367	148	0.1996	2646	X-RAY DIFFRACTION	100
2.8488-2.9326	0.2305	156	0.2028	2661	X-RAY DIFFRACTION	100
2.9326-3.0271	0.2392	133	0.2019	2717	X-RAY DIFFRACTION	100
3.0271-3.1353	0.2131	153	0.2033	2680	X-RAY DIFFRACTION	100
3.1353-3.2607	0.2203	151	0.192	2669	X-RAY DIFFRACTION	100
3.2607-3.4089	0.2579	158	0.1904	2672	X-RAY DIFFRACTION	100
3.4089-3.5885	0.214	157	0.1828	2698	X-RAY DIFFRACTION	100
3.5885-3.813	0.1824	147	0.1764	2682	X-RAY DIFFRACTION	100
3.813-4.1069	0.2112	155	0.1572	2684	X-RAY DIFFRACTION	100
4.1069-4.5193	0.1882	147	0.149	2705	X-RAY DIFFRACTION	100
4.5193-5.171	0.1768	155	0.1504	2728	X-RAY DIFFRACTION	100
5.171-6.5068	0.2172	141	0.1842	2725	X-RAY DIFFRACTION	100
6.5068-33.0077	0.1779	155	0.1789	2749	X-RAY DIFFRACTION	98

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	0.6817	-0.2807	0.0501	1.2621	-0.206	0.6653	-0.0401	0.2215	0.0279	0.3385	-0.1147	-0.4487	-0.1264	0.4544	-0.2179	0.3415	-0.1089	0.0521	0.5736	0.1077	0.6838	80.1854	65.7409	34.8002
2	0.7536	-0.2716	0.4497	0.4042	-0.3778	0.7135	-0.0726	0.0958	-0.0914	0.1324	-0.0222	-0.3169	0.0775	0.0321	-0.0001	0.4243	-0.0197	0.0274	0.4021	-0.0186	0.4957	65.0545	49.372	44.6909
3	1.2261	-0.1721	0.4118	0.3525	-0.1787	0.5925	-0.0773	-0.543	0.1546	0.6796	0.0084	-0.2023	-0.3267	-0.055	-0.0725	0.9006	-0.0445	-0.1329	0.5337	-0.1025	0.4642	67.8114	61.7463	79.3519
4	0.5256	0.1283	-0.2695	1.5597	-0.5629	0.82	-0.0648	-0.1349	0.2745	0.4365	-0.0526	-0.1504	-0.3802	0.0283	-0	0.5425	-0.0308	-0.068	0.3592	-0.047	0.4731	67.7496	64.244	61.1896
5	0.4374	-0.3963	-0.4161	0.8718	0.0547	0.6328	-0.0346	-0.0684	-0.3266	0.2771	-0.1094	-0.532	0.127	0.3001	-0.0003	0.3706	-0.0172	-0.0822	0.4404	0.0722	0.6494	80.5247	42.093	56.6309
6	0.7832	-0.0067	0.2483	0.5997	-0.1346	1.0581	-0.0789	0.1284	0.1497	0.1578	-0.0961	-0.3785	-0.2608	0.2426	-0.0117	0.4068	-0.0885	-0.0524	0.3601	0.0122	0.547	75.7365	59.584	51.2944
7	0.3655	0.302	0.0773	0.3977	-0.1497	1.4117	-0.2206	0.1696	0.2718	-0.0418	0.0125	-0.0846	-0.4973	-0.2501	-0.6529	0.496	-0.0135	0.0173	0.3714	0.1493	0.4638	51.0438	77.5925	28.6322
8	1.0874	-0.0053	0.5656	0.3935	-0.3699	1.221	0.0824	-0.0312	0.0685	0.3705	0.0487	-0.0138	-0.1259	-0.2576	0.0001	0.4168	-0.0174	0.0487	0.4797	-0.0124	0.4632	46.2627	55.5024	39.2766
9	0.4643	-0.5341	-0.0366	0.6521	0.1599	0.3601	0.0323	0.6877	-0.3811	-0.4866	0.0946	0.3442	0.5415	-0.5973	0.1641	0.7928	-0.2967	-0.0941	0.927	-0.1142	0.4639	34.1906	36.257	10.1159
10	1.7539	0.3387	0.1177	1.0242	0.0379	1.3343	-0.0949	0.6459	-0.1491	-0.4829	0.1796	-0.1091	0.3045	0.0054	-0.0004	0.6024	-0.0876	0.0568	0.6603	-0.0611	0.3891	47.8377	47.2357	15.0793
11	0.8287	-0.3767	-0.0719	0.6485	-0.0593	1.3185	-0.0433	0.0973	0.2151	-0.1275	0.1033	0.4521	-0.2076	-0.6467	-0.0016	0.3462	-0.0255	-0.0062	0.6783	0.1095	0.5206	26.9975	56.3618	31.1605
12	1.1428	0.0892	0.5391	0.9524	-0.18	0.6854	-0.075	0.3662	0.2395	-0.092	0.0901	-0.0827	-0.2562	0.0087	0	0.4282	-0.0259	0.037	0.4953	0.052	0.4236	51.069	64.3109	28.1712
13	0.5962	0.4005	-0.0148	0.6669	-0.0212	0.742	-0.1928	0.3667	0.3226	-0.2876	0.2203	0.2319	-0.2576	-0.2208	0.0019	0.4087	-0.0966	-0.0436	0.5986	0.1292	0.3611	35.7136	57.5623	19.1595

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 97 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 98 through 201 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 202 through 368 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 369 through 433 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 434 through 605 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 59 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 60 through 97 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 98 through 159 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 160 through 368 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 369 through 433 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 434 through 521 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 522 through 605 )

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