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- PDB-1s36: Crystal structure of a Ca2+-discharged photoprotein: Implications... -

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Entry
Database: PDB / ID: 1s36
TitleCrystal structure of a Ca2+-discharged photoprotein: Implications for the mechanisms of the calcium trigger and the bioluminescence
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / Photoprotein / obelin / bioluminescence / calcium binding / EF-hand / aequorin / 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 / 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
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsDeng, L. / Markova, S.V. / Vysotski, E.S. / Liu, Z.-J. / Lee, J. / Rose, J. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
Citation
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.
#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
DepositionJan 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: 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 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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 1.5Aug 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)22,7785
Polymers22,2161
Non-polymers5624
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.445, 53.445, 144.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Obelin / OBL


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: pET19b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q27709

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Non-polymers , 5 types, 149 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE / Coelenteramide


Mass: 411.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21N3O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 277 K / Method: modified microbatch / pH: 7.5
Details: 1.5 M tri-sodium citrate, 0.1 M Na-HEPES, pH 7.5, modified microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Nov 20, 2002 / Details: Rigaku/msc HiRes2
RadiationMonochromator: Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→72.46 Å / Num. obs: 15775 / % possible obs: 1 % / Observed criterion σ(I): -3 / Redundancy: 14.91 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.06 / Net I/σ(I): 9.37
Reflection shellResolution: 1.96→2.05 Å / Mean I/σ(I) obs: 2.11 / Num. unique all: 1982 / Rsym value: 0.19 / % possible all: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
PROTEUM PLUSdata reduction
LSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JF2

1jf2


Resolution: 1.96→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.886 / SU B: 3.274 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25922 780 5 %RANDOM
Rwork0.22278 ---
obs0.22459 14823 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 39 145 1673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211568
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9172115
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9245183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021225
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2801
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6981.5917
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28821472
X-RAY DIFFRACTIONr_scbond_it2.1563651
X-RAY DIFFRACTIONr_scangle_it3.4214.5643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.957→2.008 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.22 75
Rwork0.154 985
obs-1060

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