[English] 日本語
Yorodumi
- PDB-7bus: Chalcone synthase from Glycine max (L.) Merr (soybean) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bus
TitleChalcone synthase from Glycine max (L.) Merr (soybean)
ComponentsChalcone synthase
KeywordsTRANSFERASE / Isoflavonoid / Flavonoid / Soybean / PLANT PROTEIN
Function / homology
Function and homology information


chalcone synthase activity / chalcone synthase / naringenin-chalcone synthase activity / polyketide biosynthetic process / flavonoid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
Chalcone synthase 1 / Chalcone synthase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsImaizumi, R. / Mameda, R. / Takeshita, K. / Waki, T. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. ...Imaizumi, R. / Mameda, R. / Takeshita, K. / Waki, T. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. / Yamashita, S. / Nakayama, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03938 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
CitationJournal: Proteins / Year: 2020
Title: Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean.
Authors: Imaizumi, R. / Mameda, R. / Takeshita, K. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. / Nakayama, T. / Yamashita, S. / Waki, T.
History
DepositionApr 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chalcone synthase
B: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)89,2972
Polymers89,2972
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-13 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.760, 98.940, 159.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Chalcone synthase / / Chalcone synthase CHS1


Mass: 44648.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: ICHS1, GLYMA_08G109400 / Plasmid: pCold I / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q6X0M8, UniProt: P24826*PLUS, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30% PEG4000, 0.2M ammonium acetate and 0.1M sodium citrate (pH 5.6)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.52→159.3 Å / Num. obs: 30056 / % possible obs: 99.7 % / Redundancy: 15.4 % / CC1/2: 0.973 / Rmerge(I) obs: 0.575 / Rrim(I) all: 0.446 / Net I/σ(I): 6.56
Reflection shellResolution: 2.52→2.67 Å / Redundancy: 13.88 % / Rmerge(I) obs: 4.306 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 4702 / CC1/2: 0.201 / Rrim(I) all: 4.459 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DXA

6dxa


Resolution: 2.52→49.519 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.155 / SU B: 16.155 / SU ML: 0.312 / Average fsc free: 0.8166 / Average fsc work: 0.8289 / Cross valid method: FREE R-VALUE / ESU R: 0.694 / ESU R Free: 0.307
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2536 1492 4.972 %
Rwork0.1894 28515 -
all0.193 --
obs-30007 99.784 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.771 Å2
Baniso -1Baniso -2Baniso -3
1--5.072 Å20 Å2-0 Å2
2--3.745 Å20 Å2
3---1.328 Å2
Refinement stepCycle: LAST / Resolution: 2.52→49.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 0 262 6250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175930
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.6448442
X-RAY DIFFRACTIONr_angle_other_deg1.1521.57413806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47422.899276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.534151103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9441531
X-RAY DIFFRACTIONr_chiral_restr0.0570.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021210
X-RAY DIFFRACTIONr_nbd_refined0.1990.21257
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.25317
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22892
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0750.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.215
X-RAY DIFFRACTIONr_nbd_other0.2510.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3420.25
X-RAY DIFFRACTIONr_mcbond_it1.9743.6673170
X-RAY DIFFRACTIONr_mcbond_other1.9713.6663169
X-RAY DIFFRACTIONr_mcangle_it3.2655.4933980
X-RAY DIFFRACTIONr_mcangle_other3.2665.4943981
X-RAY DIFFRACTIONr_scbond_it2.4264.0443050
X-RAY DIFFRACTIONr_scbond_other2.4194.0433050
X-RAY DIFFRACTIONr_scangle_it4.0955.9274462
X-RAY DIFFRACTIONr_scangle_other4.0925.9274462
X-RAY DIFFRACTIONr_lrange_it6.14543.2726692
X-RAY DIFFRACTIONr_lrange_other6.1343.296671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.5850.3051120.3432086X-RAY DIFFRACTION99.9091
2.585-2.6560.3551090.3251995X-RAY DIFFRACTION99.905
2.656-2.7330.3121040.3061994X-RAY DIFFRACTION99.9048
2.733-2.8170.289910.261897X-RAY DIFFRACTION99.8493
2.817-2.910.288910.2431889X-RAY DIFFRACTION99.9495
2.91-3.0110.27880.2351797X-RAY DIFFRACTION99.7882
3.011-3.1250.303900.2021719X-RAY DIFFRACTION99.6694
3.125-3.2520.2671040.1891672X-RAY DIFFRACTION99.9437
3.252-3.3970.237720.1761606X-RAY DIFFRACTION99.7622
3.397-3.5620.317810.1881548X-RAY DIFFRACTION99.9387
3.562-3.7550.226730.1791473X-RAY DIFFRACTION99.6776
3.755-3.9820.27830.1541381X-RAY DIFFRACTION99.5241
3.982-4.2560.176670.1381324X-RAY DIFFRACTION99.7848
4.256-4.5960.204690.1121217X-RAY DIFFRACTION99.6899
4.596-5.0330.189520.1171149X-RAY DIFFRACTION99.9168
5.033-5.6250.214570.1621040X-RAY DIFFRACTION100
5.625-6.490.261460.172924X-RAY DIFFRACTION99.897
6.49-7.9370.226460.136795X-RAY DIFFRACTION99.6445
7.937-11.1750.211310.128635X-RAY DIFFRACTION99.1071
11.175-49.5190.238260.237374X-RAY DIFFRACTION97.7995

+
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