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- PDB-8cbb: Structure of homodimeric luciferase from Enhygromyxa salina -

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Basic information

Entry
Database: PDB / ID: 8cbb
TitleStructure of homodimeric luciferase from Enhygromyxa salina
ComponentsAlkanal monooxygenase alpha chain
KeywordsLUMINESCENT PROTEIN / Luciferase / monooxygenase
Function / homologybacterial luciferase / alkanal monooxygenase (FMN-linked) activity / Bacterial luciferase/NFP / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / bioluminescence / bacterial luciferase
Function and homology information
Biological speciesEnhygromyxa salina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsYudenko, A. / Remeeva, A. / Gushchin, I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Citation
Journal: Proteins / Year: 2024
Title: luxA Gene From Enhygromyxa salina Encodes a Functional Homodimeric Luciferase.
Authors: Yudenko, A. / Bazhenov, S.V. / Aleksenko, V.A. / Goncharov, I.M. / Semenov, O. / Remeeva, A. / Nazarenko, V.V. / Kuznetsova, E. / Fomin, V.V. / Konopleva, M.N. / Al Ebrahim, R. / Sluchanko, ...Authors: Yudenko, A. / Bazhenov, S.V. / Aleksenko, V.A. / Goncharov, I.M. / Semenov, O. / Remeeva, A. / Nazarenko, V.V. / Kuznetsova, E. / Fomin, V.V. / Konopleva, M.N. / Al Ebrahim, R. / Sluchanko, N.N. / Ryzhykau, Y. / Semenov, Y.S. / Kuklin, A. / Manukhov, I.V. / Gushchin, I.
#1: Journal: Biorxiv / Year: 2024
Title: luxA gene from Enhygromyxa salina encodes a functional homodimeric luciferase
Authors: Yudenko, A. / Bazhenov, S.V. / Aleksenko, V.A. / Goncharov, I.M. / Semenov, O. / Remeeva, A. / Nazarenko, V.V. / Kuznetsova, E. / Fomin, V.V. / Konopleva, M.N. / Al Ebrahim, R. / Sluchanko, ...Authors: Yudenko, A. / Bazhenov, S.V. / Aleksenko, V.A. / Goncharov, I.M. / Semenov, O. / Remeeva, A. / Nazarenko, V.V. / Kuznetsova, E. / Fomin, V.V. / Konopleva, M.N. / Al Ebrahim, R. / Sluchanko, N.N. / Ryzhykau, Y. / Semenov, Y.S. / Kuklin, A. / Manukhov, I.V. / Gushchin, I.
History
DepositionJan 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: 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 1.2Sep 4, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Nov 20, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkanal monooxygenase alpha chain
B: Alkanal monooxygenase alpha chain
C: Alkanal monooxygenase alpha chain
D: Alkanal monooxygenase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,4888
Polymers169,1044
Non-polymers3844
Water2,972165
1
A: Alkanal monooxygenase alpha chain
B: Alkanal monooxygenase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7444
Polymers84,5522
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-60 kcal/mol
Surface area27460 Å2
MethodPISA
2
C: Alkanal monooxygenase alpha chain
D: Alkanal monooxygenase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7444
Polymers84,5522
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-59 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.821, 73.374, 93.972
Angle α, β, γ (deg.)88.72, 77.93, 87.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Alkanal monooxygenase alpha chain / Luciferase


Mass: 42276.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enhygromyxa salina (bacteria) / Gene: luxA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S9XZH0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350 25%, lithium sulfate 0.2 M, BIS-TRIS 0.1 M pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.71→91.89 Å / Num. obs: 35543 / % possible obs: 97 % / Redundancy: 1.8 % / CC1/2: 0.981 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.068 / Rrim(I) all: 0.096 / Χ2: 0.35 / Net I/σ(I): 4 / Num. measured all: 63062
Reflection shellResolution: 2.71→2.84 Å / % possible obs: 96.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.218 / Num. measured all: 8436 / Num. unique obs: 4681 / CC1/2: 0.894 / Rpim(I) all: 0.218 / Rrim(I) all: 0.308 / Χ2: 0.42 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→91.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.87 / SU B: 18.929 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26877 1743 4.9 %RANDOM
Rwork0.19096 ---
obs0.19478 33799 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.378 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å21.4 Å22.21 Å2
2---0.77 Å2-0.66 Å2
3---1.09 Å2
Refinement stepCycle: 1 / Resolution: 2.71→91.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10876 0 20 165 11061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01211179
X-RAY DIFFRACTIONr_bond_other_d0.0020.01610023
X-RAY DIFFRACTIONr_angle_refined_deg0.3381.63515189
X-RAY DIFFRACTIONr_angle_other_deg0.1441.55223276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.73151384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.5451086
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.994101785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.020.21660
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0212913
X-RAY DIFFRACTIONr_gen_planes_other00.022263
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3463.9835542
X-RAY DIFFRACTIONr_mcbond_other2.3443.9835542
X-RAY DIFFRACTIONr_mcangle_it3.8475.9616915
X-RAY DIFFRACTIONr_mcangle_other3.8465.9626916
X-RAY DIFFRACTIONr_scbond_it2.6294.2435637
X-RAY DIFFRACTIONr_scbond_other2.6094.2375622
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3366.2578248
X-RAY DIFFRACTIONr_long_range_B_refined6.40151.56312505
X-RAY DIFFRACTIONr_long_range_B_other6.39451.58612492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.712→2.783 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 119 -
Rwork0.306 2470 -
obs--95.75 %

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