[English] 日本語
Yorodumi
- PDB-8eww: Structure of Arabidopsis fatty acid amide hydrolase mutant S305A -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more