[English] 日本語
Yorodumi
- PDB-5wl6: Crystal structure of chalcone isomerase engineered from ancestral... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wl6
TitleCrystal structure of chalcone isomerase engineered from ancestral inference (AncR7)
ComponentsEngineered Chalcone Isomerase AncR7
KeywordsISOMERASE / chalcone isomerase / naringenin / flavanone
Function / homology10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / 10k-s Protein, Hypothetical Protein A; Chain A / Chalcone isomerase / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBurke, J.R. / Kaltenbach, M. / Tawfik, D.S. / Noel, J.P.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Evolution of chalcone isomerase from a noncatalytic ancestor.
Authors: Kaltenbach, M. / Burke, J.R. / Dindo, M. / Pabis, A. / Munsberg, F.S. / Rabin, A. / Kamerlin, S.C.L. / Noel, J.P. / Tawfik, D.S.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 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: Engineered Chalcone Isomerase AncR7
B: Engineered Chalcone Isomerase AncR7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1855
Polymers48,0792
Non-polymers1063
Water6,395355
1
A: Engineered Chalcone Isomerase AncR7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0752
Polymers24,0391
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Engineered Chalcone Isomerase AncR7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1103
Polymers24,0391
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.180, 49.570, 63.100
Angle α, β, γ (deg.)98.68, 92.02, 107.90
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Engineered Chalcone Isomerase AncR7


Mass: 24039.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 500mM NaCl, 100mM NaCitrate tribasic dihydrate, 2% ethylene imine polymer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→62.14 Å / Num. obs: 54777 / % possible obs: 95.8 % / Redundancy: 3.8 % / Net I/σ(I): 10.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB:4DOI

4doi


Resolution: 1.6→28.137 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.05
RfactorNum. reflection% reflection
Rfree0.2116 1980 3.62 %
Rwork0.176 --
obs0.1773 54652 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→28.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 3 355 3510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113461
X-RAY DIFFRACTIONf_angle_d1.2064738
X-RAY DIFFRACTIONf_dihedral_angle_d11.951321
X-RAY DIFFRACTIONf_chiral_restr0.052557
X-RAY DIFFRACTIONf_plane_restr0.006617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.34751320.3043674X-RAY DIFFRACTION94
1.64-1.68430.30991360.27113752X-RAY DIFFRACTION95
1.6843-1.73390.31851590.25313716X-RAY DIFFRACTION95
1.7339-1.78990.29261370.22783753X-RAY DIFFRACTION95
1.7899-1.85380.25151380.2143748X-RAY DIFFRACTION95
1.8538-1.9280.26591390.22343760X-RAY DIFFRACTION95
1.928-2.01570.24751420.19773808X-RAY DIFFRACTION96
2.0157-2.1220.2311540.19263748X-RAY DIFFRACTION96
2.122-2.25490.22741240.17743856X-RAY DIFFRACTION96
2.2549-2.42890.20381460.17773764X-RAY DIFFRACTION97
2.4289-2.67310.21961490.17883841X-RAY DIFFRACTION98
2.6731-3.05960.22441440.18173848X-RAY DIFFRACTION98
3.0596-3.85310.2051430.15983866X-RAY DIFFRACTION98
3.8531-28.14120.16131370.14713538X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 24.568 Å / Origin y: -2.1054 Å / Origin z: -0.4755 Å
111213212223313233
T0.2052 Å2-0.0039 Å20.0048 Å2-0.1599 Å20.0324 Å2--0.2044 Å2
L0.5725 °20.059 °20.2985 °2-0.4285 °20.8402 °2--1.6396 °2
S0.0073 Å °0.0148 Å °0.0382 Å °0.0052 Å °0.0394 Å °-0.0243 Å °0.0567 Å °0.0356 Å °0 Å °
Refinement TLS groupSelection details: all

+
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