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- PDB-2f8p: Crystal structure of obelin following Ca2+ triggered bioluminesce... -

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Basic information

Entry
Database: PDB / ID: 2f8p
TitleCrystal structure of obelin following Ca2+ triggered bioluminescence suggests neutral coelenteramide as the primary excited state
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / helix-turn-helix / 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
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLiu, Z.J. / Stepanyuk, G.A. / Vysotski, E.S. / Lee, J. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of obelin after Ca2+-triggered bioluminescence suggests neutral coelenteramide as the primary excited state.
Authors: Liu, Z.J. / Stepanyuk, G.A. / Vysotski, E.S. / Lee, J. / Markova, S.V. / Malikova, N.P. / 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.S. / Chen, C.J. / Rose, J.P. / Lee, J. / Wang, B.C.
#2: 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.
#3: 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.
#4: 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.
#5: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of a Ca2+-discharged photoprotein: implications for mechanisms of the calcium trigger and bioluminescence
Authors: Deng, L. / Markova, S.V. / Vysotski, E.S. / Liu, Z.J. / Lee, J. / Rose, J. / Wang, B.C.
History
DepositionDec 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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 30, 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

Downloads & links

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Assembly

Deposited unit
A: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7715
Polymers22,2391
Non-polymers5324
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.260, 64.260, 63.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological assembly is a monomer

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Components

#1: Protein Obelin / OBL


Mass: 22238.904 Da / Num. of mol.: 1 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Gene: OBELIN / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: Q27709
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE


Mass: 411.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 2% PEG 400, 2.0 M ammonium sulfate, 0.1 M HEPES-Na , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 7.50

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9725
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2005
RadiationMonochromator: SI 2 2 0 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 1.87→64.28 Å / Num. obs: 17133 / % possible obs: 80.3 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.069 / Rsym value: 0.075 / Net I/σ(I): 25
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.66 / Rsym value: 0.26 / % possible all: 17.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SL7

1sl7


Resolution: 1.93→28.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.161 / SU ML: 0.095 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22997 844 5 %RANDOM
Rwork0.19043 ---
obs0.1924 15977 86.71 %-
all-17133 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.128 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.93→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 34 136 1699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9582161
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9724.69181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10215271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.043158
X-RAY DIFFRACTIONr_chiral_restr0.1130.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021246
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2776
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21092
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1620.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9361.5971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62121505
X-RAY DIFFRACTIONr_scbond_it2.6813741
X-RAY DIFFRACTIONr_scangle_it4.2434.5656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 24 -
Rwork0.25 460 -
obs--33.87 %

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