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- PDB-6dii: Structure of Arabidopsis Fatty Acid Amide Hydrolase in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 6dii
TitleStructure of Arabidopsis Fatty Acid Amide Hydrolase in Complex with methyl linolenyl fluorophosphonate
ComponentsFatty acid amide hydrolase
KeywordsHYDROLASE / 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 ...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
Chem-GJY / 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. / Tripathi, A. / Bankaitis, V. / Chapman, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1656263 United States
CitationJournal: 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
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: 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 1.2May 15, 2019Group: 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 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)839,08324
Polymers834,95012
Non-polymers4,13312
Water00
1
A: Fatty acid amide hydrolase
B: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8474
Polymers139,1582
Non-polymers6892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-17 kcal/mol
Surface area41330 Å2
MethodPISA
2
C: Fatty acid amide hydrolase
D: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8474
Polymers139,1582
Non-polymers6892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-15 kcal/mol
Surface area41550 Å2
MethodPISA
3
E: Fatty acid amide hydrolase
F: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8474
Polymers139,1582
Non-polymers6892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-17 kcal/mol
Surface area41940 Å2
MethodPISA
4
G: Fatty acid amide hydrolase
H: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8474
Polymers139,1582
Non-polymers6892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-15 kcal/mol
Surface area42430 Å2
MethodPISA
5
I: Fatty acid amide hydrolase
J: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8474
Polymers139,1582
Non-polymers6892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-17 kcal/mol
Surface area42060 Å2
MethodPISA
6
K: Fatty acid amide hydrolase
L: Fatty acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8474
Polymers139,1582
Non-polymers6892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-16 kcal/mol
Surface area42150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.577, 83.311, 272.811
Angle α, β, γ (deg.)90.000, 110.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 69579.141 Da / Num. of mol.: 12
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-GJY / methyl-9Z,12Z,15Z-octadecatrienylphosphonofluoridate / Methyl alpha-Linolenyl Fluorophosphonate (MLnFP)


Mass: 344.444 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C19H34FO2P
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 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

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1808 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 132397 / % possible obs: 83 % / Redundancy: 2.8 % / Biso Wilson estimate: 64.86 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.075 / Rrim(I) all: 0.132 / Χ2: 1.049 / Net I/σ(I): 6.4 / Num. measured all: 368215
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.312.30.543109000.7960.4050.6821.09569.1
3.31-3.452.30.446110880.8380.330.5581.08970
3.45-3.62.30.331111810.8930.2450.4141.07770.6
3.6-3.792.40.233114360.9510.1710.2911.08572.1
3.79-4.032.50.178118830.9710.130.2221.06674.9
4.03-4.342.60.124130060.9860.0880.1531.02981.9
4.34-4.782.80.102148700.9910.0710.1251.04493.5
4.78-5.473.20.101158340.9930.0670.1221.04899.1
5.47-6.893.40.099160280.9950.0630.1171.01899.5
6.89-503.30.042161710.9980.0270.051.02698.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DHV

6dhv


Resolution: 3.2→34.614 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.63
RfactorNum. reflection% reflection
Rfree0.2961 6719 5.14 %
Rwork0.2525 --
obs0.2547 130689 81.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 528.11 Å2 / Biso mean: 77.44 Å2 / Biso min: 6.04 Å2
Refinement stepCycle: final / Resolution: 3.2→34.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55668 0 264 0 55932
Biso mean--67.41 --
Num. residues----7275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00257126
X-RAY DIFFRACTIONf_angle_d0.47477484
X-RAY DIFFRACTIONf_chiral_restr0.0398856
X-RAY DIFFRACTIONf_plane_restr0.00710017
X-RAY DIFFRACTIONf_dihedral_angle_d9.99834611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1781-3.21420.42641390.38062724286353
3.2142-3.2520.39991870.36433452363970
3.252-3.29160.35811980.36383522372070
3.2916-3.33330.39141900.36193488367868
3.3333-3.37710.37271970.36563457365471
3.3771-3.42330.36652110.36723539375071
3.4233-3.47220.3862030.34993521372469
3.4722-3.5240.4021940.34573529372371
3.524-3.5790.38332030.323637384072
3.579-3.63760.36411960.31873596379271
3.6376-3.70020.34361800.31333630381072
3.7002-3.76740.33631930.29413685387873
3.7674-3.83980.36721760.28623696387273
3.8398-3.91810.33621980.28783773397174
3.9181-4.00320.32672150.26723888410377
4.0032-4.09610.29511940.25013955414978
4.0961-4.19840.27912080.2394144435281
4.1984-4.31170.26182480.23674284453285
4.3117-4.43830.26232640.22474504476890
4.4383-4.58130.27382300.21794771500194
4.5813-4.74460.27022520.2094853510596
4.7446-4.93410.2422810.21565029531098
4.9341-5.1580.25952800.21824987526799
5.158-5.42890.27112760.21095019529599
5.4289-5.76760.26412760.21525062533899
5.7676-6.21060.2632800.21395068534899
6.2106-6.83120.25723010.21515061536299
6.8312-7.80980.25062900.20675051534199
7.8098-9.80240.25072270.18515153538098
9.8024-34.61580.24972320.21793892412473

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