[English] 日本語
Yorodumi
- PDB-5wys: luciferase with inhibitor 3i -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wys
Titleluciferase with inhibitor 3i
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / luciferase / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / bioluminescence / peroxisome / protein-folding chaperone binding / ATP binding / metal ion binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-7V6 / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.999 Å
AuthorsGu, L. / Su, J. / Wang, F.
CitationJournal: Anal. Chem. / Year: 2017
Title: Inhibiting Firefly Bioluminescence by Chalcones
Authors: Zhang, H. / Su, J. / Lin, Y. / Bai, H. / Liu, J. / Chen, H. / Du, L. / Gu, L. / Li, M.
History
DepositionJan 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1032
Polymers60,8191
Non-polymers2841
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22420 Å2
Unit cell
Length a, b, c (Å)118.141, 118.141, 96.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 60818.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08659, firefly luciferase
#2: Chemical ChemComp-7V6 / 5-[(3R)-3-(4-boranylphenyl)-3-oxidanyl-propyl]-2-oxidanyl-benzoic acid


Mass: 284.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17BO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8 / Details: 0.5 M Li2SO4, 15% PEG8000, 0.1 M Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: MACSCIENCE / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.999→44.55 Å / Num. obs: 14133 / % possible obs: 100 % / Redundancy: 0.1285 % / Net I/σ(I): 25.53

-
Processing

Software
NameVersionClassification
PHENIX(1.10pre_2124: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementResolution: 2.999→44.547 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2696 1416 10.02 %
Rwork0.1954 --
obs0.2029 14133 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.999→44.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 21 0 4226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014321
X-RAY DIFFRACTIONf_angle_d1.1425854
X-RAY DIFFRACTIONf_dihedral_angle_d15.5262583
X-RAY DIFFRACTIONf_chiral_restr0.063660
X-RAY DIFFRACTIONf_plane_restr0.007752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9988-3.1060.3771390.22981248X-RAY DIFFRACTION99
3.106-3.23030.35961370.24921232X-RAY DIFFRACTION100
3.2303-3.37730.38741380.24381250X-RAY DIFFRACTION100
3.3773-3.55520.33551390.21341256X-RAY DIFFRACTION100
3.5552-3.77790.29061390.19221248X-RAY DIFFRACTION100
3.7779-4.06940.25411410.18271264X-RAY DIFFRACTION100
4.0694-4.47860.21041410.16481269X-RAY DIFFRACTION100
4.4786-5.12580.21591420.16041281X-RAY DIFFRACTION100
5.1258-6.45490.2411450.20311300X-RAY DIFFRACTION100
6.4549-44.55170.25561550.19761369X-RAY DIFFRACTION99

+
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