[English] 日本語
Yorodumi
- PDB-2qx7: Structure of Eugenol Synthase from Ocimum basilicum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qx7
TitleStructure of Eugenol Synthase from Ocimum basilicum
ComponentsEugenol synthase 1
KeywordsPLANT PROTEIN / eugenol / phenylpropene / PIP reductase / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


eugenol synthase / eugenol biosynthetic process / oxidoreductase activity / nucleotide binding / protein homodimerization activity
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Eugenol synthase 1
Similarity search - Component
Biological speciesOcimum basilicum (sweet basil)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsLouie, G.V. / Noel, J.P. / Bowman, M.E.
CitationJournal: Plos One / Year: 2007
Title: Structure and reaction mechanism of basil eugenol synthase
Authors: Louie, G.V. / Baiga, T.J. / Bowman, M.E. / Koeduka, T. / Taylor, J.H. / Spassova, S.M. / Pichersky, E. / Noel, J.P.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eugenol synthase 1
B: Eugenol synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4664
Polymers71,9792
Non-polymers1,4872
Water9,854547
1
A: Eugenol synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7332
Polymers35,9891
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eugenol synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7332
Polymers35,9891
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.340, 85.930, 99.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer (half of the asymmetric unit)

-
Components

#1: Protein Eugenol synthase 1 /


Mass: 35989.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ocimum basilicum (sweet basil) / Gene: EGS1 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15GI4
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium succinate, 21% PEG 3350, 0.3 M KCl, 2 mM dithiothreitol, 5 mM NADP+, pH 5.5, vapor diffusion, hanging drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2005
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.75 Å / Num. obs: 68896 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.99 % / Biso Wilson estimate: 26.18 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.54
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.83 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3 / Num. measured obs: 55088 / Num. unique obs: 9455 / % possible all: 99.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.568 / Cor.coef. Fo:Fc: 0.495
Highest resolutionLowest resolution
Rotation3 Å50.15 Å
Translation3 Å50.15 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QYC

1qyc


Resolution: 1.75→42.05 Å / FOM work R set: 0.744 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3472 5 %random
Rwork0.227 ---
obs-68894 99.9 %-
Solvent computationBsol: 50.005 Å2
Displacement parametersBiso mean: 24.074 Å2
Baniso -1Baniso -2Baniso -3
1-0.728 Å20 Å20 Å2
2--5.984 Å20 Å2
3----6.712 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 96 547 5597
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.8012
X-RAY DIFFRACTIONc_scbond_it2.7832.5
X-RAY DIFFRACTIONc_mcangle_it2.5443
X-RAY DIFFRACTIONc_scangle_it4.0554
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_angle_deg1.31
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2nap.par
X-RAY DIFFRACTION3water_rep.param

+
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