[English] 日本語
Yorodumi
- PDB-1eyp: CHALCONE ISOMERASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eyp
TitleCHALCONE ISOMERASE
ComponentsCHALCONE-FLAVONONE ISOMERASE 1
KeywordsISOMERASE / chalcone isomerase
Function / homology
Function and homology information


chalcone isomerase / chalcone isomerase activity / flavonoid biosynthetic process
Similarity search - Function
Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase superfamily / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A ...Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase superfamily / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chalcone--flavanone isomerase 1
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsJez, J.M. / Bowman, M.E. / Dixon, R.A. / Noel, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase.
Authors: Jez, J.M. / Bowman, M.E. / Dixon, R.A. / Noel, J.P.
History
DepositionMay 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHALCONE-FLAVONONE ISOMERASE 1
B: CHALCONE-FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)47,7022
Polymers47,7022
Non-polymers00
Water1,67593
1
A: CHALCONE-FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)23,8511
Polymers23,8511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHALCONE-FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)23,8511
Polymers23,8511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.370, 90.370, 352.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein CHALCONE-FLAVONONE ISOMERASE 1 / CHALCONE ISOMERASE 1


Mass: 23851.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: P28012, chalcone isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.36 Å3/Da / Density % sol: 71.77 %
Crystal growTemperature: 302 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% glycerol 1.8 M ammonium sulfate 0.05 M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 302K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
225 %(v/v)glycerol1reservoir
31.8-2.0 Mammonium sulfate1reservoir
40.05 MPIPES1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.5→38.1 Å / Num. all: 30687 / Num. obs: 27821 / % possible obs: 90.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.4
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.407 / Num. unique all: 3726 / % possible all: 71.8
Reflection
*PLUS
Num. measured all: 86781
Reflection shell
*PLUS
% possible obs: 61.7 % / Mean I/σ(I) obs: 2

-
Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→38.1 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1355 -random
Rwork0.249 ---
all-30687 --
obs-27821 90.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 0 93 3271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
X-RAY DIFFRACTIONo_angle_deg2
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 38.1 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.235 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg2

+
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://pdbjlvh1.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