[English] 日本語
Yorodumi
- PDB-6avw: Crystal structure of Arabidopsis thaliana SOBER1 L63A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6avw
TitleCrystal structure of Arabidopsis thaliana SOBER1 L63A
ComponentsCarboxylesterase SOBER1
KeywordsHYDROLASE / alpha/beta hydrolase / plant deacetylase / hypersensitive response
Function / homology
Function and homology information


short-chain carboxylesterase activity / regulation of plant-type hypersensitive response / phosphatidic acid biosynthetic process / defense response to other organism / A2-type glycerophospholipase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / fatty acid metabolic process / defense response to bacterium
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Carboxylesterase SOBER1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14449449385 Å
AuthorsBurger, M. / Willige, B.C. / Chory, J.
CitationJournal: Nat Commun / Year: 2017
Title: A hydrophobic anchor mechanism defines a deacetylase family that suppresses host response against YopJ effectors.
Authors: Burger, M. / Willige, B.C. / Chory, J.
History
DepositionSep 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carboxylesterase SOBER1


Theoretical massNumber of molelcules
Total (without water)24,9801
Polymers24,9801
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.590, 51.550, 76.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Carboxylesterase SOBER1 / Phospholipase A2 SOBER1 / Protein SUPPRESSOR OF AVRBST-ELICITED RESISTANCE 1


Mass: 24980.492 Da / Num. of mol.: 1 / Mutation: L63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOBER1, At4g22305 / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q84WK4, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.79 Å3/Da / Density % sol: 31.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 2% (v/v) PEG 400, 2 M Ammonium sulfate.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→42.67 Å / Num. obs: 10296 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 26.6700938185 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1427 / Net I/σ(I): 11.31
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.5133 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1013 / CC1/2: 0.918

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.10.1_2155)refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AVV

6avv


Resolution: 2.14449449385→42.6637328517 Å / SU ML: 0.143629684421 / Cross valid method: FREE R-VALUE / σ(F): 1.3379039537 / Phase error: 22.3510265789
RfactorNum. reflection% reflection
Rfree0.225902830899 515 5.00583203733 %
Rwork0.18777063894 --
obs0.189700656712 10288 99.8737986603 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.2234603403 Å2
Refinement stepCycle: LAST / Resolution: 2.14449449385→42.6637328517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 0 104 1714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002542277367221655
X-RAY DIFFRACTIONf_angle_d0.5800594154872253
X-RAY DIFFRACTIONf_chiral_restr0.0426384951318248
X-RAY DIFFRACTIONf_plane_restr0.00471320659064290
X-RAY DIFFRACTIONf_dihedral_angle_d16.4401817049975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1445-2.36030.2619665808241260.1867213678662395X-RAY DIFFRACTION99.881141046
2.3603-2.70180.2765691266951260.2023641104372410X-RAY DIFFRACTION99.803227076
2.7018-3.40370.227836095331270.1912299508382427X-RAY DIFFRACTION99.9217527387
3.4037-42.67220.1983670714071360.1811598341842541X-RAY DIFFRACTION99.9253452781

+
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