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- PDB-1qv0: Atomic resolution structure of obelin from Obelia longissima -

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Basic information

Entry
Database: PDB / ID: 1qv0
TitleAtomic resolution structure of obelin from Obelia longissima
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / Photoprotein / obelin / bioluminescence / atomic resolution / calcium binding / EF-hand
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: 1.1 Å
AuthorsLiu, Z.J. / Vysotski, E.S. / Deng, L. / Lee, J. / Rose, J. / Wang, B.C.
Citation
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.
#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. / 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. / 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. / Liu, Z.-J. / Markova, S. / Malikova, N. / 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. / Liu, Z.-J. / Markova, S. / Blinks, J. / Deng, L. / Frank, L. / Herko, M. / Malikova, N. / Rose, J. / Wang, B.-C. / Lee, J.
History
DepositionAug 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 16, 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)22,9436
Polymers22,2391
Non-polymers7055
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.088, 54.111, 52.535
Angle α, β, γ (deg.)90.00, 112.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1073-

HOH

21A-1165-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Obelin / OBL


Mass: 22238.904 Da / Num. of mol.: 1
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, Renilla-type luciferase

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.01 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG8000, potassium phosphate, hexaminecobaltic chloride , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Details: Vysotski, E.S., (2001) Acta Crystallogr., D57, 1919.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMpotassium/sodium phosphate1drop
21 mMEDTA1droppH7.4
38-10 mg/mlprotein1drop
423 %PEG80001reservoir
550 mM1reservoirpH5.8KH2PO4
60.1 M1reservoirHCC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / 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: 1.1→50 Å / Num. all: 86186 / Num. obs: 85842 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.1→1.16 Å / Rmerge(I) obs: 0.096 / % possible all: 99

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EL4

1el4


Resolution: 1.1→10 Å / Num. parameters: 15166 / Num. restraintsaints: 18501 / 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 0.0153
RfactorNum. reflection% reflectionSelection details
Rfree0.1609 6073 8.7 %RANDOM
Rwork0.1495 ---
all-76386 --
obs-70313 92 %-
Displacement parametersBiso mean: 10.468 Å2
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 1382 / Occupancy sum non hydrogen: 1783.07
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 43 233 1767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0227
X-RAY DIFFRACTIONs_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.05
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.161 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg3.4
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg21
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.66

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