[English] 日本語
Yorodumi
- PDB-7qxq: Coelenteramide-bound Renilla-type luciferase (AncFT) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qxq
TitleCoelenteramide-bound Renilla-type luciferase (AncFT)
ComponentsFragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
KeywordsOXIDOREDUCTASE / luciferase / coelenteramide / Renilla-like / engineered ancestor
Function / homologyChem-CEI
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.251 Å
AuthorsMarek, M. / Schenkmayerova, A.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation22-09853S Czech Republic
CitationJournal: Nat Catal / Year: 2023
Title: Catalytic mechanism for Renilla-type luciferases
Authors: Schenkmayerova, A. / Toul, M. / Pluskal, D. / Baatallah, R. / Gagnot, G. / Pinto, G.P. / Santana, V.T. / Stuchla, M. / Neugebauer, P. / Chaiyen, P. / Damborsky, J. / Bednar, D. / Janin, Y.L. ...Authors: Schenkmayerova, A. / Toul, M. / Pluskal, D. / Baatallah, R. / Gagnot, G. / Pinto, G.P. / Santana, V.T. / Stuchla, M. / Neugebauer, P. / Chaiyen, P. / Damborsky, J. / Bednar, D. / Janin, Y.L. / Prokop, Z. / Marek, M.
History
DepositionJan 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
B: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
C: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1946
Polymers107,9603
Non-polymers1,2343
Water4,954275
1
A: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3982
Polymers35,9871
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3982
Polymers35,9871
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3982
Polymers35,9871
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.224, 83.332, 102.017
Angle α, β, γ (deg.)90.000, 91.890, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)


Mass: 35986.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: Renilla-type luciferase
#2: Chemical ChemComp-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE


Mass: 411.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: magnesium acetate, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.9 Å / Num. obs: 75744 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 4404 / CC1/2: 0.594

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S97

6s97


Resolution: 2.251→44.891 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1920 4.93 %
Rwork0.1715 37060 -
obs0.1749 38980 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.76 Å2 / Biso mean: 29.9928 Å2 / Biso min: 9.56 Å2
Refinement stepCycle: final / Resolution: 2.251→44.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 93 275 7598
Biso mean--36.45 29.67 -
Num. residues----888
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.251-2.30680.351310.2434253298
2.3068-2.36920.30641160.1912676100
2.3692-2.43890.29391360.17892655100
2.4389-2.51760.25521470.17872602100
2.5176-2.60760.27991500.18312657100
2.6076-2.7120.27611180.19422655100
2.712-2.83540.27871410.18272630100
2.8354-2.98480.2861160.19072655100
2.9848-3.17180.26021510.18642648100
3.1718-3.41660.24481390.17012646100
3.4166-3.76030.22591370.173267399
3.7603-4.3040.22151280.1517263899
4.304-5.42110.19441390.13722703100
5.4211-44.8910.1891710.16272690100

+
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