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- PDB-1sl9: Obelin from Obelia longissima -

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Basic information

Entry
Database: PDB / ID: 1sl9
TitleObelin from Obelia longissima
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / Photoprotein / obelin / bioluminescence / atomic resolution / calcium binding / EF-hand / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


bioluminescence / calcium ion binding
Similarity search - Function
: / EF hand / EF hand domain / EF-hand / Recoverin; domain 1 / 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 / EF hand domain / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
C2-HYDROPEROXY-COELENTERAZINE / Obelin
Similarity search - Component
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsDeng, L. / Markova, S. / Vysotski, E. / Liu, Z.-J. / Lee, J. / Rose, J. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
Citation
#1: Journal: Protein Sci. / Year: 2000
Title: Structure of the Ca2+-regulated photoprotein obelin at 1.7 resolution determined directly from its sulfur substructure
Authors: Liu, Z.-J. / Vysotski, E.S. / Chen, C.-J. / Rose, J. / Lee, J. / Wang, B.-C.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima
Authors: Vysotski, E.S. / Liu, Z.-J. / Rose, J. / Wang, B.-C. / Lee, J.
#3: Journal: FEBS Lett. / Year: 2001
Title: Structural basis for the emission of violet bioluminescence from a W92F obelin mutant
Authors: Deng, L. / Vysotski, E.S. / Liu, Z.-J. / Markova, S.V. / Malikova, N.P. / Lee, J. / Rose, J. / Wang, B.-C.
#4: Journal: Biochemistry / Year: 2003
Title: Violet Bioluminescence and Fast Kinetics from W92F Obelin: Structure-Based Proposals for the Bioluminescence Triggering and the Identification of the Emitting Species
Authors: Vysotski, E.S. / Liu, Z.-J. / Markova, S.V. / Blinks, J. / Deng, L. / Frank, L.A. / Herko, M. / Malikova, N.P. / Rose, J.P. / Wang, B.-C. / Lee, J.
#5: Journal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Atomic resolution structure of obelin: Soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine
Authors: Liu, Z.-J. / Vysotski, E.S. / Deng, L. / Lee, J. / Rose, J. / Wang, B.-C.
#6: Journal: To be Published
Title: Preparation and X-ray Crystallographic Analysis of the Ca2+-discharged Photoprotein Obelin
Authors: Deng, L. / Markova, S.V. / Vysotski, E.S. / Liu, Z.-J. / Lee, J. / Rose, J. / Wang, B.-C.
History
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6942
Polymers22,2391
Non-polymers4551
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.021, 54.341, 52.442
Angle α, β, γ (deg.)90.00, 112.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

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Components

#1: Protein Obelin / OBL


Mass: 22238.904 Da / Num. of mol.: 1 / Mutation: S163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pET19-OL8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: Q27709
#2: Chemical ChemComp-CZH / C2-HYDROPEROXY-COELENTERAZINE / 8-BENZYL-2-HYDROPEROXY-2-(4-HYDROXY-BENZYL)-6-(4-HYDROXY-PHENYL)-2H-IMIDAZO[1,2-A]PYRAZIN-3-ONE


Mass: 455.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21N3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, potassium phosphate, hexaminecobaltic chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. all: 72553 / Num. obs: 61453 / % possible obs: 84.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.17→1.21 Å / Rmerge(I) obs: 0.249 / % possible all: 65.7

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EL4

1el4


Resolution: 1.17→10 Å / Num. parameters: 14799 / Num. restraintsaints: 17990 / Isotropic thermal model: restrained / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 5238 8.7 %RANDOM
Rwork0.1565 ---
obs0.1628 46409 92 %-
all-65465 --
Displacement parametersBiso mean: 15.2 Å2
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 1378 / Occupancy sum non hydrogen: 1743.12
Refinement stepCycle: LAST / Resolution: 1.17→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 33 211 1762
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0225
X-RAY DIFFRACTIONs_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.048
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0

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