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- PDB-1uhh: Crystal structure of cp-aequorin -

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Basic information

Entry
Database: PDB / ID: 1uhh
TitleCrystal structure of cp-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-CZP / 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)44,6844
Polymers43,7852
Non-polymers8992
Water10,233568
1
A: Aequorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3422
Polymers21,8931
Non-polymers4491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aequorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3422
Polymers21,8931
Non-polymers4491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.198, 57.274, 58.191
Angle α, β, γ (deg.)72.20, 80.00, 68.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERARGARG3AA5 - 1507 - 152
211SERSERARGARG3BB5 - 1507 - 152
321LEULEUPROPRO3AA160 - 189162 - 191
421LEULEUPROPRO3BB160 - 189162 - 191
112CZPCZPCZPCZP4AC1001
212CZPCZPCZPCZP4BD2001

NCS ensembles :
ID
1
2

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Components

#1: Protein Aequorin 2 / aequorin


Mass: 21892.654 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-CZP / (8R)-8-(CYCLOPENTYLMETHYL)-2-HYDROPEROXY-2-(4-HYDROXYBENZYL)-6-(4-HYDROXYPHENYL)-7,8-DIHYDROIMIDAZO[1,2-A]PYRAZIN-3(2H) -ONE / CP-COELENETERAZINE


Mass: 449.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27N3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 1.97 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammonium sulfate, pH 7.10, 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
DetectorType: OXFORD PX210 / Detector: CCD
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→43.8 Å / Num. all: 36134 / Num. obs: 36134 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.051 / Net I/σ(I): 9.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.138 / % possible all: 95.2

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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→33.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.38 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18954 1708 5 %RANDOM
Rwork0.1422 ---
obs0.14458 32676 95.16 %-
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: 13.794 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.03 Å20.01 Å2
2--0 Å20.03 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.122 Å0.126 Å
Refinement stepCycle: LAST / Resolution: 1.8→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 64 568 3652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213166
X-RAY DIFFRACTIONr_bond_other_d0.0020.022703
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9554293
X-RAY DIFFRACTIONr_angle_other_deg0.94536322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1075376
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_restr0.1060.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023548
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02650
X-RAY DIFFRACTIONr_nbd_refined0.2280.2713
X-RAY DIFFRACTIONr_nbd_other0.2520.23031
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2386
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5540.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3990.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4940.294
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.011.51872
X-RAY DIFFRACTIONr_mcangle_it1.82422995
X-RAY DIFFRACTIONr_scbond_it3.19331294
X-RAY DIFFRACTIONr_scangle_it4.9194.51298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
22B56tight positional00.05
11A2537medium positional0.350.5
22B56tight thermal00.5
11A2537medium thermal1.062
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 100
Rwork0.199 1947

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