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- PDB-7eg3: Crystal structure of the apoAequorin complex with (S)-HM-daCTZ -

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Basic information

Entry
Database: PDB / ID: 7eg3
TitleCrystal structure of the apoAequorin complex with (S)-HM-daCTZ
ComponentsAequorin-2
KeywordsOXIDOREDUCTASE / Aequorin
Function / homology
Function and homology information


bioluminescence / calcium ion binding
Similarity search - Function
EF hand / 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
Similarity search - Domain/homology
Chem-J2U / Aequorin-2
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsTomabechi, Y. / Shirouzu, M.
CitationJournal: Plos One / Year: 2021
Title: Chiral deaza-coelenterazine analogs for probing a substrate-binding site in the Ca2+-binding photoprotein aequorin.
Authors: Inouye, S. / Sumida, Y. / Tomabechi, Y. / Taguchi, J. / Shirouzu, M. / Hosoya, T.
History
DepositionMar 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Aequorin-2
D: Aequorin-2
E: Aequorin-2
F: Aequorin-2
G: Aequorin-2
H: Aequorin-2
I: Aequorin-2
J: Aequorin-2
K: Aequorin-2
L: Aequorin-2
M: Aequorin-2
N: Aequorin-2
O: Aequorin-2
P: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,43432
Polymers360,70616
Non-polymers6,72816
Water25,0951393
1
A: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,5441
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.800, 98.020, 121.420
Angle α, β, γ (deg.)77.630, 73.230, 75.220
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aequorin-2 /


Mass: 22544.117 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P02592
#2: Chemical
ChemComp-J2U / (2~{S})-6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-4-(phenylmethyl)-2,3-dihydroinden-1-one


Mass: 420.499 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C29H24O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.9 M (NH4)2SO4, 0.2 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→45.88 Å / Num. obs: 219672 / % possible obs: 97.4 % / Redundancy: 3.903 % / Biso Wilson estimate: 35.487 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.094 / Χ2: 0.951 / Net I/σ(I): 11.64 / Num. measured all: 857325
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.09-2.223.8170.4373.2813007936450340800.9030.50793.5
2.22-2.373.9570.2894.8613186934266333280.9660.33597.3
2.37-2.563.9530.1986.7112310631898311420.9730.22997.6
2.56-2.813.9420.1379.1511339929362287660.9840.15998
2.81-3.143.9240.0912.9810229726525260720.9920.10498.3
3.14-3.623.8740.0618.898944323416230890.9950.0798.6
3.62-4.433.8480.05223.187518319786195400.9950.0698.8
4.43-6.233.8940.04624.595919715328152030.9960.05399.2
6.23-45.883.8750.04424.9432752858984520.9960.05198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation9.48 Å46.84 Å
Translation9.48 Å46.84 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.6.0phasing
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ej3

1ej3


Resolution: 2.09→45.88 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 1997 0.91 %
Rwork0.2177 217446 -
obs0.2179 219443 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.47 Å2 / Biso mean: 35.1868 Å2 / Biso min: 13.2 Å2
Refinement stepCycle: final / Resolution: 2.09→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24376 0 512 1393 26281
Biso mean--26.01 35.29 -
Num. residues----3046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.150.27711300.2475141691429989
2.15-2.20.25111420.2458154961563897
2.2-2.270.32191430.251155181566197
2.27-2.340.28121440.2437155511569597
2.34-2.430.2951410.2386154581559997
2.43-2.520.28651450.2377156661581198
2.52-2.640.28061420.2374155711571398
2.64-2.780.24841450.2324156441578998
2.78-2.950.29131430.2392156891583298
2.95-3.180.25021430.2317156931583698
3.18-3.50.2231460.2213157891593599
3.5-4.010.24061450.2043157161586199
4.01-5.050.21991450.1867158181596399
5.05-45.880.19571430.1892156681581198

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