[English] 日本語
Yorodumi
- PDB-9em3: OPR3 wild type in its monomeric form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9em3
TitleOPR3 wild type in its monomeric form
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / ene-reductase / Old Yellow Enzyme
Function / homology
Function and homology information


12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / jasmonic acid biosynthetic process / oxylipin biosynthetic process / peroxisome / FMN binding / identical protein binding
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsBijelic, A. / Macheroux, P. / Kerschbaumer, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Sci Rep / Year: 2024
Title: Analysis of homodimer formation in 12-oxophytodienoate reductase 3 in solutio and crystallo challenges the physiological role of the dimer.
Authors: Kerschbaumer, B. / Macheroux, P. / Bijelic, A.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9763
Polymers44,4011
Non-polymers5752
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.260, 89.840, 48.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein 12-oxophytodienoate reductase 3 / 12-oxophytodienoate-10 / 11-reductase 3 / OPDA-reductase 3 / LeOPR3


Mass: 44401.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: OPR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FEW9, 12-oxophytodienoate reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES/Tris (6.5), 10 mM ammonium sulfate, 8-16% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.27→42.94 Å / Num. obs: 48983 / % possible obs: 97.49 % / Redundancy: 3 % / Biso Wilson estimate: 30.21 Å2 / CC1/2: 0.95 / Rpim(I) all: 0.25 / Net I/σ(I): 2.72
Reflection shellResolution: 2.27→2.41 Å / Num. unique obs: 8108 / CC1/2: 0.19 / Rpim(I) all: 1.27

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→42.94 Å / SU ML: 0.2536 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 897 5 %
Rwork0.2129 17026 -
obs0.2153 17923 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.23 Å2
Refinement stepCycle: LAST / Resolution: 2.27→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 39 70 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422874
X-RAY DIFFRACTIONf_angle_d0.75063916
X-RAY DIFFRACTIONf_chiral_restr0.0525434
X-RAY DIFFRACTIONf_plane_restr0.0047505
X-RAY DIFFRACTIONf_dihedral_angle_d14.50611027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.410.28851460.25672769X-RAY DIFFRACTION97.39
2.41-2.60.35231460.26252778X-RAY DIFFRACTION97.47
2.6-2.860.32861460.27262769X-RAY DIFFRACTION96.01
2.86-3.270.29981500.23642843X-RAY DIFFRACTION98.13
3.27-4.120.22821510.18892879X-RAY DIFFRACTION98.47
4.13-42.940.20931580.17392988X-RAY DIFFRACTION97.46
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)
10.761622710134-0.3046613821370.1807878721060.8595090649510.07713728285810.878699856605-0.00720588815807-0.0250885647676-0.053048585080.009124385368050.02127748498060.08832097979740.0376581776793-0.0459646029276-0.00633613592060.175386189864-0.01763670503610.02915037484030.19433267491-0.007027095826370.19338608874115.48220.9682.258
20.909822751730.05151995351330.6472916206321.959449305-0.2777665022491.60678416981-0.0815132601001-0.05976018763140.2525666455230.2468346800260.0656628744787-0.185119107884-0.08870688223320.04223846706320.008531537562040.258352173472-0.001350779293160.008994248307950.1715807576360.001078698695750.22213756672920.19336.6831.949
31.08468837675-0.3327244501160.1974545091771.35472559828-0.1583308589430.51358763041-0.0787997559286-0.04494717932040.1414080417770.1028944199930.00906293171443-0.208636710167-0.008220262421570.1437348915910.05844126495390.2313107699010.00490646354563-0.0189058773340.259309894265-0.02314587500250.19286967694232.44622.64112.176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:229 )A10 - 229
2X-RAY DIFFRACTION2( CHAIN A AND RESID 230:311 )A230 - 311
3X-RAY DIFFRACTION3( CHAIN A AND RESID 312:396 )A312 - 396

+
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