[English] 日本語
Yorodumi
- PDB-5wx4: Alkylquinolone synthase from Evodia rutaecarpa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wx4
TitleAlkylquinolone synthase from Evodia rutaecarpa
Componentsalkylquinolone synthase
KeywordsTRANSFERASE / polyketidesynthase
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkylquinolone synthase
Similarity search - Component
Biological speciesTetradium ruticarpum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.203 Å
AuthorsMatsui, T. / Kodama, T. / Tadakoshi, T. / Morita, H.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: 2-Alkylquinolone alkaloid biosynthesis in the medicinal plant Evodia rutaecarpa involves collaboration of two novel type III polyketide synthases
Authors: Matsui, T. / Kodama, T. / Mori, T. / Tadakoshi, T. / Noguchi, H. / Abe, I. / Morita, H.
History
DepositionJan 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alkylquinolone synthase
B: alkylquinolone synthase
C: alkylquinolone synthase


Theoretical massNumber of molelcules
Total (without water)136,5603
Polymers136,5603
Non-polymers00
Water5,368298
1
A: alkylquinolone synthase

A: alkylquinolone synthase


Theoretical massNumber of molelcules
Total (without water)91,0402
Polymers91,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area5980 Å2
ΔGint-23 kcal/mol
Surface area26990 Å2
MethodPISA
2
B: alkylquinolone synthase
C: alkylquinolone synthase


Theoretical massNumber of molelcules
Total (without water)91,0402
Polymers91,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-24 kcal/mol
Surface area26880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.470, 106.880, 84.380
Angle α, β, γ (deg.)90.000, 113.890, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid PROA
21chain B and segid PROB
31chain C and segid A00Z

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid PROAA0
211chain B and segid PROBB0
311chain C and segid A00ZC0

-
Components

#1: Protein alkylquinolone synthase


Mass: 45520.020 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetradium ruticarpum (plant) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0A1W7GKH4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence database references for this protein does not currently exist in the UniProt database. ...The sequence database references for this protein does not currently exist in the UniProt database. This sequence has already been deposited to GenBank as LC208544. Residues from MET (-11) to SER 0 are expression tags.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 0.2 M Magnesium chloride, 10%(w/v) PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 69341 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.2
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.3 / % possible all: 98.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.83 Å48.39 Å
Translation3.83 Å48.39 Å

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASER2.5.6phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WD8

3wd8


Resolution: 2.203→38.738 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.44
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 3465 5 %Random
Rwork0.1788 ---
obs0.1807 69330 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.07 Å2 / Biso mean: 33.888 Å2 / Biso min: 19.06 Å2
Refinement stepCycle: final / Resolution: 2.203→38.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9111 0 0 298 9409
Biso mean---31.2 -
Num. residues----1174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099300
X-RAY DIFFRACTIONf_angle_d1.14512587
X-RAY DIFFRACTIONf_chiral_restr0.0481399
X-RAY DIFFRACTIONf_plane_restr0.0061642
X-RAY DIFFRACTIONf_dihedral_angle_d14.1673467
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5567X-RAY DIFFRACTION5.573TORSIONAL
12B5567X-RAY DIFFRACTION5.573TORSIONAL
13C5567X-RAY DIFFRACTION5.573TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2027-2.23280.28051330.25682539267295
2.2328-2.26470.31151390.22726302769100
2.2647-2.29850.24261370.221826092746100
2.2985-2.33440.29871390.221726312770100
2.3344-2.37270.32551380.219826332771100
2.3727-2.41360.24431380.221826282766100
2.4136-2.45750.29641380.219826192757100
2.4575-2.50480.24391380.218426182756100
2.5048-2.55590.2721390.213126342773100
2.5559-2.61140.26471380.201426222760100
2.6114-2.67220.24111390.203726372776100
2.6722-2.7390.24381390.212626502789100
2.739-2.8130.22551380.210626282766100
2.813-2.89580.28881380.214226222760100
2.8958-2.98920.25521380.202626112749100
2.9892-3.0960.26541400.200526592799100
3.096-3.21990.21591390.201826532792100
3.2199-3.36630.24061390.190326262765100
3.3663-3.54370.23231380.182526342772100
3.5437-3.76560.19551400.166726512791100
3.7656-4.0560.20561380.155926262764100
4.056-4.46370.15951410.139326752816100
4.4637-5.10830.1521390.134126462785100
5.1083-6.43120.17191410.152226742815100
6.4312-38.74360.151410.13412710285199

+
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