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- PDB-8ey9: Structure of Arabidopsis fatty acid amide hydrolase mutant S305A ... -

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Basic information

Entry
Database: PDB / ID: 8ey9
TitleStructure of Arabidopsis fatty acid amide hydrolase mutant S305A in complex with 9-hydroxy-10,12-octadecadienoyl-ethanolamide
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 / endoplasmic reticulum ...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 / endoplasmic reticulum / Golgi apparatus / plasma membrane
Similarity search - Function
Amidase / Amidase, conserved site / Amidases signature. / Amidase signature domain / Amidase signature (AS) superfamily / Amidase
Similarity search - Domain/homology
: / Fatty acid amide hydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 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)836,79518
Polymers834,75812
Non-polymers2,0376
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9032
Polymers69,5631
Non-polymers3401
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


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9032
Polymers69,5631
Non-polymers3401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9032
Polymers69,5631
Non-polymers3401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9032
Polymers69,5631
Non-polymers3401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9032
Polymers69,5631
Non-polymers3401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9032
Polymers69,5631
Non-polymers3401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: 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
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


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)222.906, 82.908, 271.784
Angle α, β, γ (deg.)90.000, 109.130, 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-X4X / (9R,10E,12Z)-9-hydroxy-N-(2-hydroxyethyl)octadeca-10,12-dienamide


Mass: 339.513 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H37NO3 / 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: 2.9 Å3/Da / Density % sol: 57.5 %
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: 3.59→39.79 Å / Num. obs: 108547 / % possible obs: 98.5 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.163 / Net I/σ(I): 4.2
Reflection shellResolution: 3.59→3.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4896 / CC1/2: 0.837 / % possible all: 91.3

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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: 3.59→39.79 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3046 1982 1.85 %
Rwork0.2689 104930 -
obs0.2696 106912 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 387.65 Å2 / Biso mean: 91.4405 Å2 / Biso min: 44 Å2
Refinement stepCycle: final / Resolution: 3.59→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55386 0 144 0 55530
Biso mean--69.28 --
Num. residues----7242
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 (%)
3.59-3.680.34421260.35127052717893
3.68-3.780.33611510.3237632778399
3.78-3.890.35231450.31387516766198
3.89-4.020.32911450.30237518766398
4.02-4.160.36451330.28537605773898
4.16-4.330.35041460.2727536768298
4.33-4.530.33221420.25977420756297
4.53-4.770.27941280.2547424755296
4.77-5.060.27431510.25637633778499
5.06-5.450.29861490.25547672782199
5.45-60.29381420.27517636777899
6-6.870.27311430.2657678782198
6.87-8.630.25121460.22837633777997
8.64-39.790.27281350.23186975711086
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)
10.50330.2052-0.21110.462-0.41251.28890.0005-0.0957-0.01730.4601-0.09640.1662-0.0918-0.10570.03381.2858-0.07660.10010.19490.04850.5325-93.193916.0873.2426
21.2084-0.0347-0.35681.2388-0.71441.99880.02980.3091-0.09350.2091-0.18590.20790.3875-0.19080.18540.97160.02160.13320.5098-0.01460.6177-98.693713.2585-43.4379
30.28120.1491-0.27280.6564-0.41920.8219-0.2351-0.31560.34410.65310.5332-0.8657-0.30450.68430.17330.66410.1528-0.35760.8748-0.40750.6052-153.838515.6832-40.0001
41.38440.0532-0.48081.303-0.47811.0306-0.21380.4408-0.0869-0.25590.2089-0.36040.15990.1514-0.10470.8155-0.37050.1240.9303-0.29610.6384-158.123912.8908-86.7569
51.27330.1209-0.16660.6456-0.62261.4752-0.0621-0.35150.08570.38090.0714-0.0670.029-0.0193-0.01180.4804-0.0105-0.01830.3424-0.05060.4527-213.639412.7643-80.8739
61.0924-0.16480.22451.22660.032.35620.04820.2283-0.115-0.1016-0.20370.22980.2873-0.2906-0.03840.1569-0.02560.0950.26360.02980.3871-215.575810.3089-128.0098
71.2009-0.1096-0.34430.9765-0.19882.20330.01950.1355-0.0094-0.24330.03230.1493-0.1317-0.4011-0.04630.6131-0.0292-0.04010.59320.01660.6156-84.806754.0196-132.8654
80.63450.1753-0.29051.3414-1.03252.67640.0466-0.17830.10370.3181-0.02430.1221-0.2886-0.0756-0.03070.68750.02590.05940.6708-0.04440.6605-82.574651.759-85.725
91.3581-0.3569-0.47071.29330.39982.2635-0.020.2136-0.0163-0.19520.14890.3515-0.1936-0.211-0.09940.65340.0561-0.04850.66320.04030.775-249.305954.1929-89.934
101.13840.14510.09781.9106-0.52512.5143-0.0425-0.5366-0.41330.5150.09870.18720.3725-0.0492-0.02370.81240.15790.09290.99230.09850.9057-246.493751.8252-42.7769
111.4936-0.0949-0.06572.5335-0.00570.9052-0.35850.1935-0.0105-0.4890.82640.5027-0.3494-0.3106-0.23280.79660.0717-0.04131.06560.23340.7276-190.141756.8413-46.9217
120.85560.2536-0.18640.7121-0.10270.0541-0.1309-0.8913-0.26411.30150.45880.3372-0.5735-0.60960.01021.86720.76430.29521.39250.16190.793-184.671854.2982-0.1431
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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