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- PDB-1jf0: The Crystal Structure of Obelin from Obelia geniculata at 1.82 A ... -

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Basic information

Entry
Database: PDB / ID: 1jf0
TitleThe Crystal Structure of Obelin from Obelia geniculata at 1.82 A 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 / 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 / EF hand / 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: 1.82 Å
AuthorsDeng, L. / Vysotski, E. / Liu, Z.-J. / Markova, S. / Lee, J. / Rose, J. / Wang, B.-C.
Citation
Journal: To be Published
Title: The Crystal Structure of Obelin from Obelia geniculata at 1.82 Angstrom Resolution
Authors: Deng, L. / Vysotski, E. / Liu, Z.-J. / Markova, S. / Lee, J. / Rose, J. / Wang, B.-C.
#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 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)22,6432
Polymers22,1881
Non-polymers4551
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.502, 67.823, 69.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Obelin


Mass: 22187.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pET19-OG / 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.: 111 / 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: 1.77 Å3/Da / Density % sol: 30.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 8000, potassium phosphate, hexaminecobaltic chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→28 Å / Num. all: 14737 / Num. obs: 14015 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 28.19
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 10 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.8 / % possible all: 93.9

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EL4

1el4


Resolution: 1.82→19.63 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 244092.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1123 8 %RANDOM
Rwork0.212 ---
all0.22 14737 --
obs0.212 14015 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.17 Å2 / ksol: 0.4181 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.82→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 34 111 1673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.871.5
X-RAY DIFFRACTIONc_mcangle_it2.932
X-RAY DIFFRACTIONc_scbond_it3.272
X-RAY DIFFRACTIONc_scangle_it4.92.5
LS refinement shellResolution: 1.82→1.93 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 180 8 %
Rwork0.269 2061 -
obs-2061 92.8 %

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