[English] 日本語
Yorodumi
- PDB-9hly: Crystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hly
TitleCrystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (At-FatA) complexed with N-(3-chlorophenyl)-2-[4-(2-fluorophenyl)-3-methoxy-5-oxo-2H-pyrrol-1-yl]-2-methyl-propanamide
ComponentsOleoyl-acyl carrier protein thioesterase 1, chloroplastic
KeywordsHYDROLASE / Arabidopsis / Thioesterase / Inhibitor / Complex
Function / homology
Function and homology information


oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / chloroplast / fatty acid biosynthetic process
Similarity search - Function
Acyl-ACP thioesterase / Acyl-[acyl-carrier-protein] hydrolase FATA/B / : / Acyl-ACP thioesterase N-terminal domain / Acyl-ACP thioesterase C-terminal domain / HotDog domain superfamily
Similarity search - Domain/homology
: / Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMontgomery, M.G.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (At-FatA) complexed with N-(3-chlorophenyl)-2-[4-(2-fluorophenyl)-3-methoxy-5-oxo-2H-pyrrol-1-yl]-2-methyl-propanamide
Authors: Montgomery, M.G.
History
DepositionDec 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AaA: Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
BaB: Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2296
Polymers67,2312
Non-polymers9984
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-30 kcal/mol
Surface area22740 Å2
Unit cell
Length a, b, c (Å)97.670, 98.040, 127.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Oleoyl-acyl carrier protein thioesterase 1, chloroplastic / 18:0-acyl-carrier protein thioesterase / 18:0-ACP thioesterase / Acyl-[acyl-carrier-protein] hydrolase


Mass: 33615.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FATA, FATA1, At3g25110, MJL12.5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q42561, oleoyl-[acyl-carrier-protein] hydrolase
#2: Chemical ChemComp-A1IV8 / ~{N}-(3-chlorophenyl)-2-[4-(2-fluorophenyl)-3-methoxy-5-oxidanylidene-2~{H}-pyrrol-1-yl]-2-methyl-propanamide


Mass: 402.847 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20ClFN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH4.6, 1.7M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8984 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8984 Å / Relative weight: 1
ReflectionResolution: 1.96→48.83 Å / Num. obs: 44063 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rrim(I) all: 0.068 / Net I/σ(I): 14.8
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3209 / CC1/2: 0.7 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→48.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: FREE R-VALUE / ESU R: 0.184 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2722 2149 4.877 %
Rwork0.2221 41912 -
all0.225 --
obs-44061 99.862 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.951 Å2
Baniso -1Baniso -2Baniso -3
1-0.539 Å20 Å20 Å2
2---4.369 Å2-0 Å2
3---3.83 Å2
Refinement stepCycle: LAST / Resolution: 1.96→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4177 0 66 29 4272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134324
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173951
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6525870
X-RAY DIFFRACTIONr_angle_other_deg2.3311.589144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2445513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73421.789246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19215754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6661536
X-RAY DIFFRACTIONr_chiral_restr0.0730.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024798
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02926
X-RAY DIFFRACTIONr_nbd_refined0.1940.2767
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.23668
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22032
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.248
X-RAY DIFFRACTIONr_nbd_other0.2240.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0570.22
X-RAY DIFFRACTIONr_mcbond_it4.1365.3382070
X-RAY DIFFRACTIONr_mcbond_other4.1355.3362069
X-RAY DIFFRACTIONr_mcangle_it5.7737.992577
X-RAY DIFFRACTIONr_mcangle_other5.7727.9932578
X-RAY DIFFRACTIONr_scbond_it4.7595.9612253
X-RAY DIFFRACTIONr_scbond_other4.7365.9582246
X-RAY DIFFRACTIONr_scangle_it7.0888.7123293
X-RAY DIFFRACTIONr_scangle_other7.0758.7063282
X-RAY DIFFRACTIONr_lrange_it9.04860.9684625
X-RAY DIFFRACTIONr_lrange_other9.03460.9764624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0110.4671780.4263027X-RAY DIFFRACTION99.658
2.011-2.0660.3571610.3992966X-RAY DIFFRACTION99.8404
2.066-2.1260.4541230.3722923X-RAY DIFFRACTION99.6076
2.126-2.1910.3721430.3292815X-RAY DIFFRACTION99.8313
2.191-2.2630.3551240.3152755X-RAY DIFFRACTION99.8266
2.263-2.3420.3171420.3022643X-RAY DIFFRACTION100
2.342-2.430.3571340.2832572X-RAY DIFFRACTION99.9261
2.43-2.5290.3381690.2732415X-RAY DIFFRACTION99.9227
2.529-2.6410.2651210.2412371X-RAY DIFFRACTION100
2.641-2.770.2681000.2252300X-RAY DIFFRACTION99.9584
2.77-2.9190.303910.2222169X-RAY DIFFRACTION99.9116
2.919-3.0950.28890.2212064X-RAY DIFFRACTION100
3.095-3.3080.296890.2151926X-RAY DIFFRACTION99.9504
3.308-3.5720.272960.2071830X-RAY DIFFRACTION100
3.572-3.9110.256780.2011688X-RAY DIFFRACTION99.9434
3.911-4.3690.206750.1721503X-RAY DIFFRACTION99.9367
4.369-5.0380.194820.1661337X-RAY DIFFRACTION99.7189
5.038-6.1540.215760.1991144X-RAY DIFFRACTION100
6.154-8.6340.295460.195912X-RAY DIFFRACTION99.7917
8.634-48.830.335320.212552X-RAY DIFFRACTION99.6587

+
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