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- PDB-1uhi: Crystal structure of i-aequorin -

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Basic information

Entry
Database: PDB / ID: 1uhi
TitleCrystal structure of i-aequorin
ComponentsAequorin 2
KeywordsLUMINESCENT PROTEIN / 4 EF-hand motif / Complex
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
Chem-CZI / Aequorin-2
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsToma, S. / Chong, K.T. / Nakagawa, A. / Teranishi, K. / Inouye, S. / Shimomura, O.
CitationJournal: Protein Sci. / Year: 2005
Title: The crystal structures of semi-synthetic aequorins
Authors: Toma, S. / Chong, K.T. / Nakagawa, A. / Teranishi, K. / Inouye, S. / Shimomura, O.
History
DepositionJul 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn / struct_ncs_dom_lim / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: Aequorin 2
B: Aequorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4514
Polymers43,3162
Non-polymers1,1352
Water8,791488
1
A: Aequorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2262
Polymers21,6581
Non-polymers5671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aequorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2262
Polymers21,6581
Non-polymers5671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.263, 54.432, 57.523
Angle α, β, γ (deg.)102.05, 99.70, 103.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPRO2AA5 - 807 - 82
21SERSERPROPRO2BB5 - 807 - 82
32GLNGLNARGARG2AA120 - 150122 - 152
42GLNGLNARGARG2BB120 - 150122 - 152
53PHEPHEPROPRO2AA172 - 189174 - 191
63PHEPHEPROPRO2BB172 - 189174 - 191
74ALAALAASPASP3AA81 - 11983 - 121
84ALAALAASPASP3BB81 - 11983 - 121

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Components

#1: Protein Aequorin 2 / / aequorin


Mass: 21658.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: PIP-HE / Production host: Escherichia coli (E. coli) / References: UniProt: P02592
#2: Chemical ChemComp-CZI / (2R)-8-BENZYL-2-HYDROPEROXY-6-(4-HYDROXYPHENYL)-2-(4-IODOBENZYL)-7,8-DIHYDROIMIDAZO[1,2-A]PYRAZIN-3(2H)-ONE / I-COELENETERAZINE


Mass: 567.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H22IN3O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 1.98 Å3/Da / Density % sol: 37.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→33.27 Å / Num. all: 35601 / Num. obs: 35601 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.077 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rsym value: 0.147 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EJ3

1ej3


Resolution: 1.8→33.27 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.881 / SU B: 3.495 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25035 1743 5.1 %RANDOM
Rwork0.18805 ---
obs0.19126 32560 96.35 %-
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: 15.305 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 68 488 3576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213170
X-RAY DIFFRACTIONr_bond_other_d0.0030.022695
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9564297
X-RAY DIFFRACTIONr_angle_other_deg1.0536296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3645376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023562
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02660
X-RAY DIFFRACTIONr_nbd_refined0.2490.2884
X-RAY DIFFRACTIONr_nbd_other0.2590.23235
X-RAY DIFFRACTIONr_nbtor_other0.090.21657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3170.2350
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5420.2177
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4460.2197
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5910.2178
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0191.51872
X-RAY DIFFRACTIONr_mcangle_it1.69122995
X-RAY DIFFRACTIONr_scbond_it2.99431298
X-RAY DIFFRACTIONr_scangle_it4.5344.51302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
965tight positional0.080.05
1125medium positional0.260.5
390loose positional0.285
965tight thermal0.310.5
1125medium thermal0.962
390loose thermal1.6310
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 118
Rwork0.213 2394

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