PDB-1mt5: CRYSTAL STRUCTURE OF FATTY ACID AMIDE HYDROLASE

ID or keywords:

Entry

Database: PDB / ID: 1mt5

Title

CRYSTAL STRUCTURE OF FATTY ACID AMIDE HYDROLASE

Components

Fatty-acid amide hydrolase

Keywords

HYDROLASE / AMIDASE SIGNATURE

Function / homology

Function and homology information

Arachidonate metabolism / fatty acid amide hydrolase / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / monoacylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Bracey, M.H. / Hanson, M.A. / Masuda, K.R. / Stevens, R.C. / Cravatt, B.F.

Citation

Journal: science / Year: 2002
Title: Structural Adaptations in a Membrane Enzyme That Terminates Endocannabinoid Signaling
Authors: Bracey, M.H. / Hanson, M.A. / Masuda, K.R. / Stevens, R.C. / Cravatt, B.F.

History

Deposition	Sep 20, 2002	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2002	Provider: repository / Type: Initial release
Revision 1.1	Apr 28, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Apr 3, 2024	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_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1mt5.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb1mt5.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	1mt5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1mt5_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	1mt5_full_validation.pdf.gz	1.2 MB	Display
Data in XML	1mt5_validation.xml.gz	162 KB	Display
Data in CIF	1mt5_validation.cif.gz	247.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mt/1mt5 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/1mt5	HTTPS FTP

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Related structure data

Similar structure data	3qj9-d 3pr0-d 4hbp-d 3ppm-d 3lj6-d 2vya-d 3k83-d 3oj8-d 3k84-d 2wj1-d 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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fatty-acid amide hydrolase

B: Fatty-acid amide hydrolase

C: Fatty-acid amide hydrolase

D: Fatty-acid amide hydrolase

E: Fatty-acid amide hydrolase

F: Fatty-acid amide hydrolase

G: Fatty-acid amide hydrolase

H: Fatty-acid amide hydrolase

I: Fatty-acid amide hydrolase

J: Fatty-acid amide hydrolase

K: Fatty-acid amide hydrolase

L: Fatty-acid amide hydrolase

M: Fatty-acid amide hydrolase

N: Fatty-acid amide hydrolase

O: Fatty-acid amide hydrolase

P: Fatty-acid amide hydrolase

hetero molecules

949 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fatty-acid amide hydrolase

B: Fatty-acid amide hydrolase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Fatty-acid amide hydrolase

D: Fatty-acid amide hydrolase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Fatty-acid amide hydrolase

F: Fatty-acid amide hydrolase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Fatty-acid amide hydrolase

H: Fatty-acid amide hydrolase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Fatty-acid amide hydrolase

J: Fatty-acid amide hydrolase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Fatty-acid amide hydrolase

L: Fatty-acid amide hydrolase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

M: Fatty-acid amide hydrolase

N: Fatty-acid amide hydrolase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

O: Fatty-acid amide hydrolase

P: Fatty-acid amide hydrolase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	147.107, 272.019, 147.216
Angle α, β, γ (deg.)	90.00, 115.21, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	THR	THR	5	A	A	37 - 573	1 - 537
2	1	ALA	ALA	THR	THR	5	B	B	37 - 573	1 - 537
3	1	ALA	ALA	THR	THR	5	C	C	37 - 573	1 - 537
4	1	ALA	ALA	THR	THR	5	D	D	37 - 573	1 - 537
5	1	ALA	ALA	THR	THR	5	E	E	37 - 573	1 - 537
6	1	ALA	ALA	THR	THR	5	F	F	37 - 573	1 - 537
7	1	ALA	ALA	THR	THR	5	G	G	37 - 573	1 - 537
8	1	ALA	ALA	THR	THR	5	H	H	37 - 573	1 - 537
9	1	ALA	ALA	THR	THR	5	I	I	37 - 573	1 - 537
10	1	ALA	ALA	THR	THR	5	J	J	37 - 573	1 - 537
11	1	ALA	ALA	THR	THR	5	K	K	37 - 573	1 - 537
12	1	ALA	ALA	THR	THR	5	L	L	37 - 573	1 - 537
13	1	ALA	ALA	THR	THR	5	M	M	37 - 573	1 - 537
14	1	ALA	ALA	THR	THR	5	N	N	37 - 573	1 - 537
15	1	ALA	ALA	THR	THR	5	O	O	37 - 573	1 - 537
16	1	ALA	ALA	THR	THR	5	P	P	37 - 573	1 - 537
17	2	MAY	MAY	MAY	MAY	1	A	Q	600
18	2	MAY	MAY	MAY	MAY	1	B	R	600
19	2	MAY	MAY	MAY	MAY	1	C	S	600
20	2	MAY	MAY	MAY	MAY	1	D	T	600
21	2	MAY	MAY	MAY	MAY	1	E	U	600
22	2	MAY	MAY	MAY	MAY	1	F	V	600
23	2	MAY	MAY	MAY	MAY	1	G	W	600
24	2	MAY	MAY	MAY	MAY	1	H	X	600
25	2	MAY	MAY	MAY	MAY	1	I	Y	600
26	2	MAY	MAY	MAY	MAY	1	J	Z	600
27	2	MAY	MAY	MAY	MAY	1	K	AA	600
28	2	MAY	MAY	MAY	MAY	1	L	BA	600
29	2	MAY	MAY	MAY	MAY	1	M	CA	600
30	2	MAY	MAY	MAY	MAY	1	N	DA	600
31	2	MAY	MAY	MAY	MAY	1	O	EA	600
32	2	MAY	MAY	MAY	MAY	1	P	FA	600

#1: Protein	Fatty-acid amide hydrolase / Oleamide hydrolase / Anandamide amidohydrolase Mass: 58943.031 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FAAH / Plasmid: pTrcHis / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P97612, Hydrolases; Acting on ester bonds
#2: Chemical	ChemComp-MAY / METHYL ARACHIDONYL FLUOROPHOSPHONATE / MAFP Mass: 370.482 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₂₁H₃₆FO₂P
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.82 Å³/Da / Density % sol: 56.44 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, 2,4-methyl pentanediol, sodium citrate, lithium sulphate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal grow

*PLUS

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details
1	8 mg/ml	protein	1	drop
2	100 mM	sodium citrate	1	reservoir	pH5.
3	100 mM	lithium sulfate	1	reservoir
4	7 %(w/v)	PEG6000	1	reservoir
5	5 %(v/v)	MPD	1	reservoir
6	0-20 mM	dithiothreitol	1	reservoir

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2001
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. all: 243192 / Num. obs: 173615 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / R_sym value: 0.104 / Net I/σ(I): 4.4
Reflection	PLUS Lowest resolution: 50 Å / % possible obs: 76 % / Redundancy: 2.1 % / R_merge(I) obs*: 0.104
Reflection shell	PLUS % possible obs: 79 % / R_merge(I) obs: 0.264 / Mean I/σ(I) obs*: 2.7

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing
REFMAC	5.1.19	refinement
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: FAAH structure in an alternate spacegroup. Solved by MAD/MIRAS phasing.

Resolution: 2.8→141.42 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.887 / SU B: 19.283 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.51
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: Refinemant carried out while the manuscript was in press resulted in improved geometry at the cost of slightly higher R values. Atoms for which no density was observed were not included in ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26228	9297	5.1 %	RANDOM
R_work	0.2184	-	-	-
obs	0.22062	173616	71.37 %	-
all	-	243192	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 54.594 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.23 Å²	0 Å²	-0.94 Å²
2-	-	4.38 Å²	0 Å²
3-	-	-	-2.96 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→141.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	64140	0	384	0	64524

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	65996
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.587	1.984	89778
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.736	5	8576
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	10320
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	49656
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.126	0.3	31512
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.5	2787
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.095	0.3	71
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.143	0.5	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.952	2	42832
X-RAY DIFFRACTION	r_mcangle_it	1.671	3	68512
X-RAY DIFFRACTION	r_scbond_it	0.911	2	23164
X-RAY DIFFRACTION	r_scangle_it	1.422	3	21266
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	24	tight positional	0.04	0.05
2	B	24	tight positional	0.06	0.05
3	C	24	tight positional	0.04	0.05
4	D	24	tight positional	0.07	0.05
5	E	24	tight positional	0.06	0.05
6	F	24	tight positional	0.06	0.05
7	G	24	tight positional	0.05	0.05
8	H	24	tight positional	0.06	0.05
9	I	24	tight positional	0.05	0.05
10	J	24	tight positional	0.05	0.05
11	K	24	tight positional	0.05	0.05
12	L	24	tight positional	0.05	0.05
13	M	24	tight positional	0.06	0.05
14	N	24	tight positional	0.05	0.05
15	O	24	tight positional	0.05	0.05
16	P	24	tight positional	0.06	0.05
1	A	4008	medium positional	0.3	0.5
2	B	4008	medium positional	0.3	0.5
3	C	4008	medium positional	0.29	0.5
4	D	4008	medium positional	0.28	0.5
5	E	4008	medium positional	0.32	0.5
6	F	4008	medium positional	0.31	0.5
7	G	4008	medium positional	0.29	0.5
8	H	4008	medium positional	0.3	0.5
9	I	4008	medium positional	0.28	0.5
10	J	4008	medium positional	0.3	0.5
11	K	4008	medium positional	0.3	0.5
12	L	4008	medium positional	0.3	0.5
13	M	4008	medium positional	0.46	0.5
14	N	4008	medium positional	0.34	0.5
15	O	4008	medium positional	0.29	0.5
16	P	4008	medium positional	0.31	0.5
1	A	24	tight thermal	0.08	0.5
2	B	24	tight thermal	0.08	0.5
3	C	24	tight thermal	0.09	0.5
4	D	24	tight thermal	0.07	0.5
5	E	24	tight thermal	0.08	0.5
6	F	24	tight thermal	0.07	0.5
7	G	24	tight thermal	0.07	0.5
8	H	24	tight thermal	0.1	0.5
9	I	24	tight thermal	0.1	0.5
10	J	24	tight thermal	0.07	0.5
11	K	24	tight thermal	0.11	0.5
12	L	24	tight thermal	0.09	0.5
13	M	24	tight thermal	0.17	0.5
14	N	24	tight thermal	0.18	0.5
15	O	24	tight thermal	0.09	0.5
16	P	24	tight thermal	0.07	0.5
1	A	4008	medium thermal	0.84	2
2	B	4008	medium thermal	0.67	2
3	C	4008	medium thermal	0.92	2
4	D	4008	medium thermal	0.92	2
5	E	4008	medium thermal	0.66	2
6	F	4008	medium thermal	0.78	2
7	G	4008	medium thermal	0.72	2
8	H	4008	medium thermal	0.89	2
9	I	4008	medium thermal	0.65	2
10	J	4008	medium thermal	0.67	2
11	K	4008	medium thermal	0.63	2
12	L	4008	medium thermal	0.69	2
13	M	4008	medium thermal	1.42	2
14	N	4008	medium thermal	1.22	2
15	O	4008	medium thermal	0.62	2
16	P	4008	medium thermal	0.75	2

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.35	728
R_work	0.279	12811

Refinement

*PLUS

Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. reflection obs: 173615 / R_factor R_free: 0.237 / R_factor R_work: 0.2

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.029
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.041

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