[English] 日本語
Yorodumi
- PDB-1icq: CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1icq
TitleCRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO COMPLEXED WITH 9R,13R-OPDA
Components12-OXOPHYTODIENOATE REDUCTASE 1
KeywordsOXIDOREDUCTASE / beta-alpha-barrel / PROTEIN-FMN-(9R / 13R-OPDA)-complex / FMN-SUBSTRATE-complex
Function / homology
Function and homology information


12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / oxylipin biosynthetic process / fatty acid biosynthetic process / FMN binding / oxidoreductase activity / cytoplasm
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 9R,13R-12-OXOPHYTODIENOIC ACID / 12-oxophytodienoate reductase 1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBreithaupt, C. / Strassner, J. / Breitinger, U. / Huber, R. / Macheroux, P. / Schaller, A. / Clausen, T.
CitationJournal: Structure / Year: 2001
Title: X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.
Authors: Breithaupt, C. / Strassner, J. / Breitinger, U. / Huber, R. / Macheroux, P. / Schaller, A. / Clausen, T.
History
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN THE THREE LAST CARBONS OF THE PENTENYL CHAIN OF 9R,13R-OPDA ARE DISORDERED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 12-OXOPHYTODIENOATE REDUCTASE 1
B: 12-OXOPHYTODIENOATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3846
Polymers84,8862
Non-polymers1,4984
Water5,711317
1
A: 12-OXOPHYTODIENOATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1923
Polymers42,4431
Non-polymers7492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-OXOPHYTODIENOATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1923
Polymers42,4431
Non-polymers7492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.583, 72.759, 72.616
Angle α, β, γ (deg.)62.42, 85.19, 79.96
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein 12-OXOPHYTODIENOATE REDUCTASE 1 / OPR1


Mass: 42443.035 Da / Num. of mol.: 2 / Mutation: R142M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: OPR1 / Plasmid: PGEX-G / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9XG54, 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-OPD / 9R,13R-12-OXOPHYTODIENOIC ACID / 9R,13R-OPDA


Mass: 292.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H28O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Tris/HCl, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMMOPS-KOH1drop
3100 mMTris-HCl1reservoir
41.45 Mammonium sulfate1reservoir
52 %PEG4001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2000 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 54064 / % possible obs: 83.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1790 / % possible all: 54.6
Reflection
*PLUS
Num. measured all: 99966
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 54.6 %

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb: 1ICP

1icp


Resolution: 2→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.234 2717 RANDOM
Rwork0.198 --
obs-53641 -
Displacement parametersBiso mean: 37.1 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 98 317 5973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.35
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.96
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

+
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