[English] 日本語
Yorodumi
- PDB-8qmx: OPR3 wildtype in complex with NADPH4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qmx
TitleOPR3 wildtype in complex with NADPH4
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / Old Yellow Enzyme / ene-reductase / flavoenzyme / NADPH
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
Chem-5J8 / FLAVIN MONONUCLEOTIDE / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBijelic, A. / Macheroux, P. / Kerschbaumer, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Febs J. / Year: 2024
Title: Loop 6 and the beta-hairpin flap are structural hotspots that determine cofactor specificity in the FMN-dependent family of ene-reductases.
Authors: Kerschbaumer, B. / Totaro, M.G. / Friess, M. / Breinbauer, R. / Bijelic, A. / Macheroux, P.
History
DepositionSep 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 12-oxophytodienoate reductase 3
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0808
Polymers88,8022
Non-polymers3,2776
Water11,962664
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4755
Polymers44,4011
Non-polymers2,0734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6053
Polymers44,4011
Non-polymers1,2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.640, 89.850, 81.130
Angle α, β, γ (deg.)90.00, 104.92, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-5J8 / [[(2R,3S,4R,5R)-5-(5-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 747.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H32N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES/Tris, 50 mM ammonium sulfate, 12% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.4→47.34 Å / Num. obs: 155161 / % possible obs: 98.99 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.67
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 5129 / CC1/2: 0.553

-
Processing

Software
NameVersionClassification
PHENIX(dev_4761: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.34 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 7758 5 %
Rwork0.182 --
obs0.1831 155161 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5671 0 214 664 6549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136047
X-RAY DIFFRACTIONf_angle_d1.3768253
X-RAY DIFFRACTIONf_dihedral_angle_d16.0092162
X-RAY DIFFRACTIONf_chiral_restr0.09904
X-RAY DIFFRACTIONf_plane_restr0.0111042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.35252560.35164874X-RAY DIFFRACTION99
1.42-1.430.3372570.33694880X-RAY DIFFRACTION99
1.43-1.450.33572590.32434937X-RAY DIFFRACTION99
1.45-1.470.31682560.30574860X-RAY DIFFRACTION99
1.47-1.490.33212570.29334909X-RAY DIFFRACTION99
1.49-1.510.2932580.28014893X-RAY DIFFRACTION99
1.51-1.530.27962580.27094890X-RAY DIFFRACTION99
1.53-1.550.26462540.2564826X-RAY DIFFRACTION97
1.55-1.580.26782540.25114829X-RAY DIFFRACTION98
1.58-1.60.25162620.23024971X-RAY DIFFRACTION99
1.6-1.630.22612560.21414867X-RAY DIFFRACTION99
1.63-1.660.24622620.21184962X-RAY DIFFRACTION99
1.66-1.690.22232590.20464918X-RAY DIFFRACTION99
1.69-1.730.22332590.19544916X-RAY DIFFRACTION99
1.73-1.760.21682580.19634912X-RAY DIFFRACTION99
1.76-1.80.23362610.19064954X-RAY DIFFRACTION99
1.8-1.850.21052570.18934876X-RAY DIFFRACTION99
1.85-1.90.21112580.18514909X-RAY DIFFRACTION99
1.9-1.960.19392590.18514913X-RAY DIFFRACTION99
1.96-2.020.20712590.18824916X-RAY DIFFRACTION99
2.02-2.090.21982570.18564894X-RAY DIFFRACTION98
2.09-2.180.20742550.18114831X-RAY DIFFRACTION97
2.18-2.270.21862620.18364984X-RAY DIFFRACTION100
2.27-2.390.20842600.18334946X-RAY DIFFRACTION100
2.39-2.540.2032620.18444978X-RAY DIFFRACTION100
2.54-2.740.20962600.18324935X-RAY DIFFRACTION99
2.74-3.020.22462600.18334949X-RAY DIFFRACTION99
3.02-3.450.17722610.17284952X-RAY DIFFRACTION99
3.45-4.350.15812550.1444839X-RAY DIFFRACTION97
4.35-47.340.17052670.15085083X-RAY DIFFRACTION100

+
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