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- PDB-6abh: Structure of a natural red emitting luciferase from Phrixothrix h... -

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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, C-terminal domain superfamily / AMP-binding enzyme / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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