[English] 日本語
Yorodumi
- PDB-7yj7: Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yj7
TitleCrystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) complex with Naringenin
Componentschalcone synthase 1 (ScCHS1)
KeywordsTRANSFERASE / flavonoids biosynthesis / chalcone synthase / Stenoloma chusanum
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / NARINGENIN
Function and homology information
Biological speciesOdontosoria chusana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsLi, J.X. / Cheng, A.X. / Zhang, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770330 China
National Natural Science Foundation of China (NSFC)32000228 China
National Natural Science Foundation of China (NSFC)31870720 China
CitationJournal: J Integr Plant Biol / Year: 2022
Title: Molecular and structural characterization of a promiscuous chalcone synthase from the fern species Stenoloma chusanum.
Authors: Ni, R. / Niu, M. / Fu, J. / Tan, H. / Zhu, T.T. / Zhang, J. / Lou, H.X. / Zhang, P. / Li, J.X. / Cheng, A.X.
History
DepositionJul 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: chalcone synthase 1 (ScCHS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7782
Polymers44,5061
Non-polymers2721
Water4,576254
1
A: chalcone synthase 1 (ScCHS1)
hetero molecules

A: chalcone synthase 1 (ScCHS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5574
Polymers89,0122
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area6790 Å2
ΔGint-16 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.426, 72.294, 82.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

21A-718-

HOH

-
Components

#1: Protein chalcone synthase 1 (ScCHS1)


Mass: 44506.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odontosoria chusana (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.997→32.713 Å / Num. obs: 24501 / % possible obs: 89.9 % / Redundancy: 12 % / CC1/2: 0.989 / Net I/σ(I): 20.8
Reflection shellResolution: 1.997→2.069 Å / Num. unique obs: 1774 / CC1/2: 0.937

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VEY

7vey


Resolution: 1.997→32.713 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 2000 8.16 %
Rwork0.1756 22501 -
obs0.1774 24501 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.91 Å2 / Biso mean: 28.3034 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 1.997→32.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 20 254 3246
Biso mean--29.02 32.73 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013059
X-RAY DIFFRACTIONf_angle_d1.0144154
X-RAY DIFFRACTIONf_chiral_restr0.118471
X-RAY DIFFRACTIONf_plane_restr0.005530
X-RAY DIFFRACTIONf_dihedral_angle_d19.2071118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9973-2.04730.22741010.1811113365
2.0473-2.10260.18431100.1695124571
2.1026-2.16450.21411180.1857132775
2.1645-2.23430.21961230.1751138479
2.2343-2.31410.20841320.1793147884
2.3141-2.40680.221400.182158290
2.4068-2.51630.22981510.1899169595
2.5163-2.64890.24821550.1951175099
2.6489-2.81470.20651580.19381770100
2.8147-3.03190.19671590.18451788100
3.0319-3.33680.20351590.17981797100
3.3368-3.8190.19811610.1651804100
3.819-4.80910.18481630.15291832100
4.8091-32.7130.15781700.1771191699

+
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