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- PDB-1sl7: Crystal structure of calcium-loaded apo-obelin from Obelia longissima -

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Basic information

Entry
Database: PDB / ID: 1sl7
TitleCrystal structure of calcium-loaded apo-obelin from Obelia longissima
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / Photoprotein / obelin / bioluminescence / calcium binding / EF-hand / aequorin / fluorescence / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Protein Sci. / Year: 2005
Title: All three Ca2+-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin.
Authors: Deng, L. / Vysotski, E.S. / Markova, S.V. / 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
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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

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Assembly

Deposited unit
A: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3764
Polymers22,2561
Non-polymers1203
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.641, 58.641, 110.378
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 / OBL


Mass: 22255.891 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 277 K / Method: modified microbatch / pH: 7.5
Details: 20% w/v polyethylene glycol 10000, 0.1M HEPES, pH 7.5, modified microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18694 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 4.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JF2

1jf2


Resolution: 2.2→51.99 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.721 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: There is a block of density in the vicinity of Trp 179, Trp 114 and HOH 1, indicating that a small solvent molecule is present. The authors believe that, based on their crystallization set ...Details: There is a block of density in the vicinity of Trp 179, Trp 114 and HOH 1, indicating that a small solvent molecule is present. The authors believe that, based on their crystallization set up, it is most likely Tris. However, it cannot be unambiguously modeled given the resolution of 2.2 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.23938 499 4.8 %RANDOM
Rwork0.18584 ---
obs0.18856 10396 99.89 %-
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: 27.934 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 3 110 1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211441
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9241946
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3775172
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_restr0.0920.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021119
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2456
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8012857
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.80831377
X-RAY DIFFRACTIONr_scbond_it2.322584
X-RAY DIFFRACTIONr_scangle_it3.2583569
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 38
Rwork0.165 709

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