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- PDB-1sl8: Calcium-loaded apo-aequorin from Aequorea victoria -

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Basic information

Entry
Database: PDB / ID: 1sl8
TitleCalcium-loaded apo-aequorin from Aequorea victoria
ComponentsAequorin 1
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 / 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 ...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 speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 1.7 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: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / 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_database_related.db_name / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Authors informed that there are several isoforms of this protein from the same species. ...SEQUENCE Authors informed that there are several isoforms of this protein from the same species. The conflict at residue 138 arises because their sequence is one of the isoforms.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aequorin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0094
Polymers21,8891
Non-polymers1203
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aequorin 1
hetero molecules

A: Aequorin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0188
Polymers43,7772
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3590 Å2
ΔGint-92 kcal/mol
Surface area17830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.371, 54.371, 135.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Aequorin 1


Mass: 21888.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pET19b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: P07164
#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


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 277 K / Method: modified microbatch / pH: 4.6
Details: 30% v/v 2-methyl-2,4-pentanediol, 0.1M sodium acetate, pH 4.6, modified microbatch, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU12.2909
SYNCHROTRONAPS 22-ID20.97
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEJan 23, 2003Rigaku/MSC CMF15-50Cr8
MAR CCD 165 mm2CCDMar 20, 2003
RadiationMonochromator: Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
12.29091
20.971
ReflectionResolution: 1.7→50 Å / Num. obs: 22954 / % possible obs: 98.8 % / Redundancy: 8.3 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.38 / Net I/σ(I): 45.9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.7 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAS / Resolution: 1.7→50.64 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.588 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23635 1176 5.1 %RANDOM
Rwork0.21573 ---
obs0.21679 21713 98.71 %-
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: 30.473 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--1.3 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 3 154 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211495
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.9282018
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1135180
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_restr0.1190.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021159
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2719
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0971.5895
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97521431
X-RAY DIFFRACTIONr_scbond_it3.2313600
X-RAY DIFFRACTIONr_scangle_it5.1974.5587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 86
Rwork0.297 1394

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