[English] 日本語
Yorodumi
- PDB-5dxy: Crystal structure of Dbr2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dxy
TitleCrystal structure of Dbr2
ComponentsArtemisinic aldehyde Delta(11(13)) reductase
KeywordsOXIDOREDUCTASE / Dbr2
Function / homology
Function and homology information


artemisinic aldehyde Delta11(13)-reductase / 12-oxophytodienoate reductase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / jasmonic acid biosynthetic process / oxylipin biosynthetic process / peroxisome / FMN binding / cytosol
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
Chem-5J8 / FLAVIN MONONUCLEOTIDE / Artemisinic aldehyde Delta(11(13)) reductase
Similarity search - Component
Biological speciesArtemisia annua (sweet wormwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLi, L. / Chen, T.T. / Xu, Y.C.
CitationJournal: to be published
Title: The Crystal structure of Dbr2
Authors: Li, L.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Artemisinic aldehyde Delta(11(13)) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6823
Polymers42,4781
Non-polymers1,2042
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-5 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.682, 80.430, 84.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Artemisinic aldehyde Delta(11(13)) reductase / Dbr2


Mass: 42478.051 Da / Num. of mol.: 1 / Mutation: M27L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artemisia annua (sweet wormwood) / Gene: DBR2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus(DE3) RIPL
References: UniProt: C5H429, artemisinic aldehyde Delta11(13)-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-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.: 1 / Source method: obtained synthetically / Formula: C21H32N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 34967 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 16.19 Å2 / Rmerge(I) obs: 0.066 / Χ2: 2.413 / Net I/av σ(I): 43.009 / Net I/σ(I): 15.7 / Num. measured all: 243177
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.77-1.86.80.29817162.06699.8
1.8-1.836.80.25817321.86599.9
1.83-1.876.80.2317042.26899.8
1.87-1.916.90.217161.76299.8
1.91-1.956.90.17317101.89399.9
1.95-1.996.90.1917433.27199.8
1.99-2.0470.15117042.58599.8
2.04-2.170.12317202.17299.9
2.1-2.1670.10817592.37899.7
2.16-2.2370.09717292.39599.9
2.23-2.3170.09417182.43999.9
2.31-2.47.10.08717362.49399.7
2.4-2.517.10.08717622.86999.8
2.51-2.647.10.08817323.5699.9
2.64-2.817.10.08817583.12299.9
2.81-3.0370.08217653.46999.9
3.03-3.3370.06517612.29899.9
3.33-3.816.80.04217842.31199.7
3.81-4.870.03318061.7999.9
4.8-506.70.02719121.18299.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.4.0phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DXX

5dxx


Resolution: 1.77→37.382 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 16.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1835 1997 5.83 %
Rwork0.153 32257 -
obs0.1548 34254 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.05 Å2 / Biso mean: 17.8274 Å2 / Biso min: 7.53 Å2
Refinement stepCycle: final / Resolution: 1.77→37.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 79 300 3203
Biso mean--21.73 25.36 -
Num. residues----365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063024
X-RAY DIFFRACTIONf_angle_d1.0384137
X-RAY DIFFRACTIONf_chiral_restr0.042454
X-RAY DIFFRACTIONf_plane_restr0.005528
X-RAY DIFFRACTIONf_dihedral_angle_d14.0391105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7703-1.81460.19681380.15392134227293
1.8146-1.86360.19421260.15852208233495
1.8636-1.91850.20171460.15912232237896
1.9185-1.98040.19691340.15652247238197
1.9804-2.05120.18371390.15222282242198
2.0512-2.13330.2051450.14982286243199
2.1333-2.23040.1761360.14892314245099
2.2304-2.34790.19191430.15542282242598
2.3479-2.4950.20541430.16222320246399
2.495-2.68760.20571410.16942334247599
2.6876-2.9580.19941490.17392325247499
2.958-3.38580.21611460.163423842530100
3.3858-4.26470.14761490.137424062555100
4.2647-37.39020.15241620.136725032665100

+
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