[English] 日本語
Yorodumi
- PDB-6abh: Structure of a natural red emitting luciferase from Phrixothrix h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6abh
TitleStructure of a natural red emitting luciferase from Phrixothrix hirtus (P1 crystal form)
ComponentsRed-bioluminescence eliciting luciferase
KeywordsLUMINESCENT PROTEIN / bioluminescence / Luciferase / Red emission
Function / homology
Function and homology information


firefly luciferase / bioluminescence / monooxygenase activity / peroxisome
Similarity search - Function
ANL, N-terminal domain / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhrixothrix hirtus (beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsCarrasco-Lopez, C. / Panjikar, S. / Naumov, P. / Rabeh, W.
Funding supportUnited Arab Emirates, 1items
OrganizationGrant numberCountry
United Arab Emirates
CitationJournal: Life Sci Alliance / Year: 2018
Title: Beetle luciferases with naturally red- and blue-shifted emission.
Authors: Carrasco-Lopez, C. / Ferreira, J.C. / Lui, N.M. / Schramm, S. / Berraud-Pache, R. / Navizet, I. / Panjikar, S. / Naumov, P. / Rabeh, W.M.
History
DepositionJul 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Red-bioluminescence eliciting luciferase
B: Red-bioluminescence eliciting luciferase
C: Red-bioluminescence eliciting luciferase
D: Red-bioluminescence eliciting luciferase
E: Red-bioluminescence eliciting luciferase
F: Red-bioluminescence eliciting luciferase
G: Red-bioluminescence eliciting luciferase
H: Red-bioluminescence eliciting luciferase


Theoretical massNumber of molelcules
Total (without water)486,6668
Polymers486,6668
Non-polymers00
Water00
1
A: Red-bioluminescence eliciting luciferase
B: Red-bioluminescence eliciting luciferase
G: Red-bioluminescence eliciting luciferase
H: Red-bioluminescence eliciting luciferase


Theoretical massNumber of molelcules
Total (without water)243,3334
Polymers243,3334
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Red-bioluminescence eliciting luciferase
D: Red-bioluminescence eliciting luciferase
E: Red-bioluminescence eliciting luciferase
F: Red-bioluminescence eliciting luciferase


Theoretical massNumber of molelcules
Total (without water)243,3334
Polymers243,3334
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.697, 121.174, 129.443
Angle α, β, γ (deg.)61.86, 68.35, 74.17
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Red-bioluminescence eliciting luciferase


Mass: 60833.215 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phrixothrix hirtus (beetle) / Plasmid: pET28 MHL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9U4U7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 19-21% PEG 3350, 0.1M Bis-tris propane (pH 6.0, supplemented with 0.2M ammonium sulfate)
PH range: 6.0-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→48.762 Å / Num. obs: 98610 / % possible obs: 94.13 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.053 / Rrim(I) all: 0.123 / Rsym value: 0.111 / Net I/σ(I): 14.5
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 2 / Num. measured obs: 76451 / Num. unique obs: 14365 / CC1/2: 0.769 / Rpim(I) all: 0.497 / Rrim(I) all: 1.163 / Rsym value: 1.046

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AAA

6aaa


Resolution: 3.05→48.762 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.07 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2854 954 1.02 %
Rwork0.2404 --
obs0.2408 93729 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→48.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25451 0 0 0 25451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01226122
X-RAY DIFFRACTIONf_angle_d1.62235403
X-RAY DIFFRACTIONf_dihedral_angle_d14.5939607
X-RAY DIFFRACTIONf_chiral_restr0.0724020
X-RAY DIFFRACTIONf_plane_restr0.0084482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0498-3.21060.39491200.363313140X-RAY DIFFRACTION93
3.2106-3.41170.3681350.333113140X-RAY DIFFRACTION93
3.4117-3.6750.31581470.285313123X-RAY DIFFRACTION93
3.675-4.04470.31441300.24113203X-RAY DIFFRACTION93
4.0447-4.62960.28011500.207612935X-RAY DIFFRACTION92
4.6296-5.83120.24451350.210213430X-RAY DIFFRACTION95
5.8312-48.76840.24551370.211213804X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 11.616 Å / Origin y: 0.873 Å / Origin z: 7.791 Å
111213212223313233
T0.5197 Å2-0.0107 Å20.0271 Å2-0.5699 Å2-0.0428 Å2--0.6326 Å2
L0.1962 °20.1769 °2-0.0359 °2-0.6765 °2-0.1532 °2--0.0636 °2
S0.0944 Å °-0.0889 Å °-0.0182 Å °0.2105 Å °-0.0565 Å °0.1025 Å °0.0021 Å °-0.011 Å °-0.0357 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