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- PDB-7o3u: The crystal structure of obelin from Obelia longissima bound with... -

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Basic information

Entry
Database: PDB / ID: 7o3u
TitleThe crystal structure of obelin from Obelia longissima bound with v-coelenterazine
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / bioluminescence / coelenterazine / v-coelenterazine / calcium binding
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
v-coelenterazine / Obelin
Similarity search - Component
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLarionova, M.D. / Wu, L.J. / Vysotski, E.S. / Liu, Z.-J.
CitationJournal: Protein Sci. / Year: 2022
Title: Crystal structure of semisynthetic obelin-v.
Authors: Larionova, M.D. / Wu, L. / Eremeeva, E.V. / Natashin, P.V. / Gulnov, D.V. / Nemtseva, E.V. / Liu, D. / Liu, Z.J. / Vysotski, E.S.
History
DepositionApr 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7583
Polymers22,2391
Non-polymers5202
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.880, 42.880, 375.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

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Components

#1: Protein Obelin / OBL


Mass: 22238.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: v-coelenterazine (v-CTZ or CTZ V) is a synthetic analogue of natural coelenterazine with an additional benzyl ring.
Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pET-19b-OL8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q27709
#2: Chemical ChemComp-V1W / v-coelenterazine


Mass: 479.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H21N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.24 Å3/Da / Density % sol: 45.09 % / Description: Light-yellow rod-shaped crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.2 M DL-Malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35638 / % possible obs: 99.5 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.106 / Net I/σ(I): 12.77
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 5610 / CC1/2: 0.896 / Rrim(I) all: 0.771 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3777refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qv0

1qv0


Resolution: 1.8→37.14 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 1809 5.08 %
Rwork0.24 33814 -
obs0.2413 35623 99.54 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.05 Å2 / Biso mean: 56.3241 Å2 / Biso min: 18.77 Å2
Refinement stepCycle: final / Resolution: 1.8→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 37 86 1641
Biso mean--29.76 53.69 -
Num. residues----189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.40071430.35952485262896
1.85-1.90.32321420.30952567270999
1.9-1.960.25111290.282326382767100
1.96-2.030.32871280.290326262754100
2.03-2.120.33161310.283126162747100
2.12-2.210.35951120.281426052717100
2.21-2.330.35551420.27826182760100
2.33-2.470.2991420.278626142756100
2.48-2.670.31341560.279826272783100
2.67-2.930.24391260.251125902716100
2.93-3.360.26671350.234126412776100
3.36-4.230.22271630.199125912754100
4.23-37.140.22711600.200525962756100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.83461.2631-3.27585.7733-2.43965.85720.2276-1.6693-0.86630.747-1.1177-0.8999-0.02822.1180.85240.6171-0.2862-0.18031.92920.65740.971930.34524.6842-9.92
22.21710.133-0.57995.0188-1.91384.1573-0.2684-0.038-0.3697-0.9235-0.1521-0.05620.53680.685-0.4980.45150.07040.10240.40950.12330.195916.76914.3841-26.062
32.91450.9537-3.00386.7988-1.11513.2078-0.30890.6751-0.0194-1.00650.69871.63822.1766-1.5537-0.80721.0713-0.319-0.35830.79980.21470.7798-0.1609-5.891-21.7407
42.46541.019-1.75334.2212-2.60013.47190.2517-0.1133-0.13540.48970.52391.1095-0.5963-0.7725-0.61210.31730.05860.05810.35090.13370.36456.01476.1703-16.364
50.1145-0.0935-0.2472.4792-2.31143.1960.1579-0.37950.05040.6822-0.6063-0.37-1.19290.98190.38380.4583-0.2332-0.06460.68170.12550.267620.09889.9707-15.0961
63.6071-0.0648-0.95246.7183-4.78183.8662-0.0135-0.2445-0.01540.121-0.14480.18280.18470.0371-0.07170.30.04180.05660.26850.09020.22410.1634-1.9831-8.1412
74.22990.73970.17273.4068-3.33336.8111-0.3445-0.2424-0.4749-0.17730.2870.16141.5256-0.6981-0.96881.20020.18170.2940.55540.1880.56675.1056-14.0025-8.8889
81.49730.0566-1.25072.5668-2.02124.4982-0.4882-0.2673-0.8186-1.0957-0.5995-0.83611.83821.4295-1.44390.94980.53270.31880.49140.25610.591518.855-10.8041-16.1861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 15 )A6 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 47 )A16 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 57 )A48 - 57
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 81 )A58 - 81
5X-RAY DIFFRACTION5chain 'A' and (resid 82 through 104 )A82 - 104
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 122 )A105 - 122
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 131 )A123 - 131
8X-RAY DIFFRACTION8chain 'A' and (resid 132 through 195 )A132 - 195

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