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- PDB-1jf2: Crystal Structure of W92F obelin mutant from Obelia longissima at... -

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Basic information

Entry
Database: PDB / ID: 1jf2
TitleCrystal Structure of W92F obelin mutant from Obelia longissima at 1.72 Angstrom resolution
Componentsobelin
KeywordsLUMINESCENT PROTEIN / bioluminescence / calcium-regulated photoprotein / obelin / obelia / hydroid
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 / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLiu, Z.-J. / Vysotski, E.S. / Deng, L. / Markova, S.V. / Lee, J. / Rose, J.P. / Wang, B.-C.
Citation
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.R. / Deng, L. / Frank, L.A. / Herko, M. / Malikova, N.P. / Rose, J.P. / Wang, B.C. / Lee, J.
#1: Journal: Protein Sci. / Year: 2000
Title: Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure.
Authors: Liu, Z.J. / Vysotski, E.S. / Chen, C.J. / Rose, J.P. / 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: Bioluminescence and Chemiluminescence 2000 / Year: 2001
Title: Obelin crystal structure: implications for the bioluminescence mechanism
Authors: Vysotski, E. / Liu, Z.-J. / Deng, L. / Rose, J. / Wang, B.-C. / Lee, J.
History
DepositionJun 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2014Group: Database references
Revision 1.4Oct 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 1.5Aug 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)22,6712
Polymers22,2161
Non-polymers4551
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.449, 53.449, 144.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein obelin


Mass: 22215.869 Da / Num. of mol.: 1 / Mutation: W92F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pOL-92F / 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.: 128 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
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
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: Deng, L., (2001) FEBS Lett., 506, 281.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-10 mg/mlprotein1drop
218 %PEG80001reservoir
350 mMpotassium phosphate1reservoir
4hexamine cobalt chloride1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 23136 / Num. obs: 21633 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.08
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.35 / % possible all: 87.7
Reflection
*PLUS
% possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EL4

1el4


Resolution: 1.72→26.28 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 259784.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1711 7.9 %RANDOM
Rwork0.232 ---
all0.245 23136 --
obs0.232 21633 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.47 Å2 / ksol: 0.4095 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→26.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 34 128 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 1.72→1.83 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 255 8 %
Rwork0.294 2914 -
obs-2914 84.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 7.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.359 / % reflection Rfree: 8 % / Rfactor Rwork: 0.294

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