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- PDB-8ey1: Structure of Arabidopsis fatty acid amide hydrolase mutant S305A ... -

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Basic information

Entry
Database: PDB / ID: 8ey1
TitleStructure of Arabidopsis fatty acid amide hydrolase mutant S305A in complex with N-(3-oxododecanoyl)-L-homoserine lactone
ComponentsFatty acid amide hydrolase
KeywordsHYDROLASE / Fatty acid amide hydrolase / mutant / Arabidopsis / lipid 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 ...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 / endoplasmic reticulum / plasma membrane
Similarity search - Function
Amidase / Amidase, conserved site / Amidases signature. / Amidase signature domain / Amidase signature (AS) superfamily / Amidase
Similarity search - Domain/homology
N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE / Fatty acid amide hydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAziz, M. / Wang, X. / Gaguancela, O.A. / Chapman, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To be published
Title: Structural interactions explain the versatility of FAAH in the hydrolysis of plant and microbial acyl amide signals
Authors: Aziz, M. / Wang, X. / Gaguancela, O.A. / Chapman, K.D.
History
DepositionOct 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)836,24517
Polymers834,75812
Non-polymers1,4875
Water00
1
A: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8612
Polymers69,5631
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8612
Polymers69,5631
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8612
Polymers69,5631
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8612
Polymers69,5631
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8612
Polymers69,5631
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)225.544, 83.750, 270.943
Angle α, β, γ (deg.)90.000, 109.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fatty acid amide hydrolase / AtFAAH / N-acylethanolamine amidohydrolase


Mass: 69563.141 Da / Num. of mol.: 12 / Mutation: S305A
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: Chemical
ChemComp-OHN / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE


Mass: 297.390 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H27NO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 293 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

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.07809 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07809 Å / Relative weight: 1
ReflectionResolution: 3.2→39.82 Å / Num. obs: 143834 / % possible obs: 91.2 % / Redundancy: 2.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Net I/σ(I): 4.2
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.388 / Num. unique obs: 6942 / CC1/2: 0.948 / % possible all: 89.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EWW

8eww


Resolution: 3.2→39.82 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 1980 1.41 %
Rwork0.2594 138764 -
obs0.2599 140744 88.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 280.38 Å2 / Biso mean: 84.9251 Å2 / Biso min: 37.89 Å2
Refinement stepCycle: final / Resolution: 3.2→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55534 0 105 0 55639
Biso mean--72.81 --
Num. residues----7260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.280.38741420.366498751001789
3.28-3.370.41291360.3471102831041993
3.37-3.470.35381390.3265102461038592
3.47-3.580.34831560.3143102311038793
3.58-3.710.31231340.3011102351036992
3.71-3.860.29221530.2725101221027592
3.86-4.030.3131350.2587101241025991
4.03-4.240.28411440.240599491009390
4.24-4.510.27611430.234100131015690
4.51-4.860.26051460.22099721986787
4.86-5.340.27031370.2317100801021790
5.34-6.120.28241460.2489100351018189
6.12-7.70.28791500.24798631001387
7.7-39.820.22451190.21597987810669
Refinement TLS params.

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

IDL11 (°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)
11.32170.0491-0.37751.9852-0.66060.3366-0.1384-0.3661-0.09740.58020.43-0.5319-0.42330.49880.06590.8718-0.199-0.10571.5154-0.41320.973211.548515.3768-81.2221
20.69760.0108-0.04330.5775-0.47640.6801-0.30210.5195-0.096-0.67060.3903-0.29880.08280.1319-0.03621.2959-0.71220.2731.4233-0.23310.90316.148213.4366-128.057
30.3225-0.0258-0.07510.9961-0.10230.27330.0115-0.2450.13070.69-0.1928-0.1305-0.30160.1021-0.32621.2031-0.16120.09220.18430.0490.5721-49.283615.983-124.0984
41.53420.142-0.26041.2853-0.27811.6188-0.05040.4541-0.07550.0204-0.08030.20470.147-0.15180.15250.60160.04440.1240.3070.02270.6068-54.41913.5779-170.8365
50.9959-0.1701-0.40772.03550.66320.745-0.11040.2071-0.0918-0.87990.40850.5479-0.3014-0.22950.02320.8166-0.1965-0.28861.28650.340.957-24.587257.4321-88.6285
60.9912-0.0303-0.0970.62160.54710.4976-0.264-0.383-0.0590.59560.44260.42610.0256-0.0599-0.05640.79310.49830.22761.49790.25620.8564-20.261955.0998-41.8298
71.2021-0.1552-0.15031.4987-0.02191.6031-0.05110.2625-0.1462-0.52080.06940.15520.00030.0462-0.01610.54850.0406-0.12830.7011-0.03710.617735.581254.8835-46.9228
80.7810.3691-0.07131.4501-0.4792.23980.1191-0.2013-0.08760.2396-0.14350.11490.11980.04040.02880.43550.07220.04850.6709-0.07070.577537.938452.30970.0204
91.63010.0286-0.54641.36090.04062.13910.0293-0.1721-0.01090.5092-0.0454-0.1905-0.1870.38270.00990.6693-0.0719-0.07660.4052-0.02740.5136-94.829812.60984.4296
100.8644-0.1101-0.32041.35840.67122.45610.00650.2504-0.006-0.2096-0.0272-0.0992-0.16470.15990.03090.5132-0.03920.07810.44980.00240.594-97.520210.3768-42.5081
111.35210.325-0.32791.3674-0.59792.15350.0883-0.23830.02340.4492-0.0212-0.1368-0.39810.2192-0.05020.6007-0.0552-0.06040.7626-0.0930.639571.425112.7864-38.0257
120.8739-0.20310.05181.63780.41362.30730.03710.18230.0108-0.4533-0.0091-0.0304-0.11320.1430.0010.425-0.01980.01730.77810.04130.635168.219210.6348-85.0022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 605)A4 - 605
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 605)B1 - 605
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 605)C4 - 605
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 605)D1 - 605
5X-RAY DIFFRACTION5(chain 'E' and resid 4 through 605)E4 - 605
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 605)F1 - 605
7X-RAY DIFFRACTION7(chain 'G' and resid 4 through 605)G4 - 605
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 605)H1 - 605
9X-RAY DIFFRACTION9(chain 'I' and resid 4 through 605)I4 - 605
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 605)J1 - 605
11X-RAY DIFFRACTION11(chain 'K' and resid 4 through 605)K4 - 605
12X-RAY DIFFRACTION12(chain 'L' and resid 1 through 605)L1 - 605

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