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

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Basic information

Entry
Database: PDB / ID: 8eww
TitleStructure of Arabidopsis fatty acid amide hydrolase mutant S305A
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
Fatty acid amide hydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 24, 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

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Assembly

Deposited unit
A: Fatty acid amide hydrolase
B: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)139,1262
Polymers139,1262
Non-polymers00
Water2,396133
1
A: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)69,5631
Polymers69,5631
Non-polymers00
Water181
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.451, 81.324, 133.180
Angle α, β, γ (deg.)90.000, 104.510, 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.: 2 / Mutation: S305A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FAAH, At5g64440, T12B11.3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7XJJ7, fatty acid amide hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50 %
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: 2.8→38.8 Å / Num. obs: 36725 / % possible obs: 98.8 % / Observed criterion σ(I): 1.4 / Redundancy: 3.5 % / CC1/2: 0.96 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4438 / CC1/2: 0.725 / % possible all: 98.1

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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: 6DHV

6dhv


Resolution: 2.8→38.78 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 1882 5.13 %
Rwork0.2342 34797 -
obs0.2355 36679 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.41 Å2 / Biso mean: 99.4568 Å2 / Biso min: 41.23 Å2
Refinement stepCycle: final / Resolution: 2.8→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9095 0 0 133 9228
Biso mean---51.13 -
Num. residues----1189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.870.38291440.36262610275497
2.87-2.960.36421430.35132672281599
2.96-3.050.30881440.33512646279098
3.05-3.160.34381420.31562618276097
3.16-3.290.34121420.29752673281598
3.29-3.440.30691420.28452673281599
3.44-3.620.27941490.26912704285399
3.62-3.850.27871420.23822672281499
3.85-4.140.20651430.21362686282999
4.14-4.560.21971460.19732668281498
4.56-5.220.24981440.20382682282699
5.22-6.570.25881530.229227352888100
6.57-38.780.2391480.2042758290698
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)
12.06930.60070.44212.5329-1.1442.09880.00920.3656-0.194-0.035-0.0532-0.6548-0.20270.82460.0171.0403-0.08430.1151.2173-0.05771.300773.912459.263439.3113
23.30730.6481.33973.0055-0.50094.27120.0534-0.6476-0.09820.89730.0635-0.467-0.47580.1652-0.08931.05710.0171-0.12650.8894-0.14040.988665.841763.575674.9775
32.45240.64450.5882.2476-0.08513.0434-0.07960.2374-0.27530.1750.103-0.7933-0.01170.4588-0.02210.7547-0.06240.01460.815-0.12331.012473.395657.187454.3423
42.5830.7891.48012.33331.4673.42420.01980.62990.01860.0179-0.0165-0.6644-0.33870.9921-0.00530.8315-0.0644-0.07270.989-0.03421.213780.548656.578659.9078
51.10810.7838-0.25951.76761.16671.9380.12120.26190.2919-0.6636-0.05750.1706-1.206-0.15620.23281.43570.09930.01191.29460.06611.28247.630776.882931.294
62.5260.89860.84012.63150.73993.3502-0.16120.9989-0.4821-0.82630.1959-0.03420.6752-0.1073-0.02981.2733-0.10150.08691.2628-0.11460.808746.228647.338917.0794
73.95610.12491.22983.73951.00762.6804-0.2020.7933-0.1871-0.71240.432-0.01780.1715-0.2357-0.1861.0729-0.25370.06351.2146-0.05560.664642.033551.57521.6863
82.14830.62020.29262.6436-0.12652.548-0.25590.77670.4226-0.88050.11620.2197-0.29650.02120.12521.0343-0.12390.00781.15470.07840.648240.97461.703825.1078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 97 )A4 - 97
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 241 )A98 - 241
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 521 )A242 - 521
4X-RAY DIFFRACTION4chain 'A' and (resid 522 through 605 )A522 - 605
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 42 )B1 - 42
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 232 )B43 - 232
7X-RAY DIFFRACTION7chain 'B' and (resid 233 through 404 )B233 - 404
8X-RAY DIFFRACTION8chain 'B' and (resid 405 through 605 )B405 - 605

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