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- PDB-8a9s: Crystal structure of Ca2+-discharged obelin in complex with coele... -

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Basic information

Entry
Database: PDB / ID: 8a9s
TitleCrystal structure of Ca2+-discharged obelin in complex with coelenteramine-v
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / bioluminescence / photoprotein / obelin / coelenterazine analogue / coelenterazine-v
Function / homology
Function and homology information


bioluminescence / calcium ion binding
Similarity search - Function
EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
3-azanyl-2-(phenylmethyl)benzo[f]quinoxalin-8-ol / Obelin
Similarity search - Component
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKovaleva, M.I. / Natashin, P.V. / Schevtsov, M.B. / Eremeeva, E.V. / Bukhdruker, S.S. / Dmitrieva, D.A. / Mishin, A.V. / Vysotski, E.S. / Borshchevskiy, V.I.
Funding support Russian Federation, 3items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Russian Science Foundation22-14-00125 Russian Federation
Russian Foundation for Basic Research20-44-240006 Russian Federation
CitationJournal: Sci Rep / Year: 2022
Title: Crystal structure of semi-synthetic obelin-v after calcium induced bioluminescence implies coelenteramine as the main reaction product.
Authors: Natashin, P.V. / Eremeeva, E.V. / Shevtsov, M.B. / Kovaleva, M.I. / Bukhdruker, S.S. / Dmitrieva, D.A. / Gulnov, D.V. / Nemtseva, E.V. / Gordeliy, V.I. / Mishin, A.V. / Borshchevskiy, V.I. / Vysotski, E.S.
History
DepositionJun 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 7, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 18, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Obelin
B: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,62712
Polymers44,5102
Non-polymers1,11710
Water6,143341
1
A: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8146
Polymers22,2551
Non-polymers5595
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8146
Polymers22,2551
Non-polymers5595
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.281, 77.281, 182.224
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Obelin / OBL


Mass: 22254.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q27709
#2: Chemical ChemComp-LK9 / 3-azanyl-2-(phenylmethyl)benzo[f]quinoxalin-8-ol


Mass: 301.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→33.46 Å / Num. obs: 35579 / % possible obs: 99.22 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1129 / Net I/σ(I): 10.07
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 3561 / CC1/2: 0.399

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EL4

1el4


Resolution: 2.1→33.46 Å / SU ML: 0.3045 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8423
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2103 716 2.01 %
Rwork0.1595 34850 -
obs0.1606 35566 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 72 341 3476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343262
X-RAY DIFFRACTIONf_angle_d0.49494415
X-RAY DIFFRACTIONf_chiral_restr0.0361442
X-RAY DIFFRACTIONf_plane_restr0.0034582
X-RAY DIFFRACTIONf_dihedral_angle_d11.13031174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.35821440.26686942X-RAY DIFFRACTION98.84
2.26-2.490.29081430.21126976X-RAY DIFFRACTION99.41
2.49-2.850.27111260.19377010X-RAY DIFFRACTION99.8
2.85-3.590.2171400.14996983X-RAY DIFFRACTION99.61
3.59-33.460.1581630.12626939X-RAY DIFFRACTION98.54

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