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- PDB-1uhk: Crystal structure of n-aequorin -

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Basic information

Entry
Database: PDB / ID: 1uhk
TitleCrystal structure of n-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-CZN / Aequorin-2
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.3Dec 27, 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 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Aequorin 2
B: Aequorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2994
Polymers43,3162
Non-polymers9832
Water8,935496
1
A: Aequorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1502
Polymers21,6581
Non-polymers4921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aequorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1502
Polymers21,6581
Non-polymers4921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.223, 57.038, 57.768
Angle α, β, γ (deg.)72.35, 79.97, 67.89
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
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
111SERSERPROPRO2AA5 - 807 - 82
211SERSERPROPRO2BB5 - 807 - 82
321GLNGLNARGARG2AA120 - 150122 - 152
421GLNGLNARGARG2BB120 - 150122 - 152
531PHEPHEPROPRO2AA172 - 189174 - 191
631PHEPHEPROPRO2BB172 - 189174 - 191
741ALAALAASPASP3AA81 - 11983 - 121
841ALAALAASPASP3BB81 - 11983 - 121
112CZNCZNCZNCZN4AC1001
212CZNCZNCZNCZN4BD2001

NCS ensembles :
ID
1
2

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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-CZN / (2S,8R)-8-BENZYL-2-HYDROPEROXY-6-(4-HYDROXYPHENYL)-2-(2-NAPHTHYLMETHYL)-7,8-DIHYDROIMIDAZO[1,2-A]PYRAZIN-3(2H)-ONE / N-COELENETERAZINE


Mass: 491.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H25N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 1.96 Å3/Da / Density % sol: 36.78 %
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: 1.6→43.5 Å / Num. all: 50773 / Num. obs: 50773 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 13.4 Å2 / Rsym value: 0.044 / Net I/σ(I): 14.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.2 % / Rsym value: 0.131 / % possible all: 79.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.68 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19854 2362 5 %RANDOM
Rwork0.16401 ---
obs0.1657 45000 93.28 %-
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: 12.765 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.03 Å20.02 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 74 496 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213206
X-RAY DIFFRACTIONr_bond_other_d0.0030.022724
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9584346
X-RAY DIFFRACTIONr_angle_other_deg0.93636364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0365380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023600
X-RAY DIFFRACTIONr_gen_planes_other0.010.02670
X-RAY DIFFRACTIONr_nbd_refined0.2270.2735
X-RAY DIFFRACTIONr_nbd_other0.2470.23192
X-RAY DIFFRACTIONr_nbtor_other0.0850.21598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2322
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.262
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7641.51892
X-RAY DIFFRACTIONr_mcangle_it1.42523026
X-RAY DIFFRACTIONr_scbond_it2.47131314
X-RAY DIFFRACTIONr_scangle_it3.9834.51320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
11965tight positional0.060.05
111125medium positional0.380.5
2260medium positional0.040.5
11390loose positional0.515
11965tight thermal0.260.5
111125medium thermal0.822
2260medium thermal0.562
11390loose thermal1.1710
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.218 129
Rwork0.231 2284

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