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- PDB-5zab: Crystal structure of cf3-aequorin -

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Basic information

Entry
Database: PDB / ID: 5zab
TitleCrystal structure of cf3-aequorin
ComponentsAequorin-2
KeywordsLUMINESCENT PROTEIN / Semi-synthetic aequorin
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-9A3 / Aequorin-2
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.147 Å
AuthorsInouye, S. / Tomabechi, Y. / Sekine, S.I. / Shirouzu, M. / Hosoya, T.
CitationJournal: J. Biochem. / Year: 2018
Title: Slow luminescence kinetics of semi-synthetic aequorin: expression, purification and structure determination of cf3-aequorin.
Authors: Inouye, S. / Tomabechi, Y. / Hosoya, T. / Sekine, S.I. / Shirouzu, M.
History
DepositionFeb 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
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)368,82532
Polymers360,70616
Non-polymers8,11916
Water25,2571402
1
A: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Aequorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0522
Polymers22,5441
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.800, 97.550, 121.840
Angle α, β, γ (deg.)77.620, 73.060, 75.170
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 189)
21(chain B and resid 2 through 189)
31(chain C and resid 2 through 189)
41(chain D and resid 2 through 189)
51(chain E and resid 2 through 189)
61(chain F and resid 2 through 189)
71(chain G and resid 2 through 189)
81(chain H and resid 2 through 189)
91(chain I and resid 2 through 189)
101(chain J and resid 2 through 189)
111chain K
121chain L
131(chain M and resid 2 through 189)
141(chain N and resid 2 through 189)
151(chain O and resid 2 through 189)
161(chain P and resid 2 through 189)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYS(chain A and resid 2 through 189)AA2 - 18911 - 198
2LYSLYS(chain B and resid 2 through 189)BB2 - 18911 - 198
3LYSLYS(chain C and resid 2 through 189)CC2 - 18911 - 198
4LYSLYS(chain D and resid 2 through 189)DD2 - 18911 - 198
5LYSLYS(chain E and resid 2 through 189)EE2 - 18911 - 198
6LYSLYS(chain F and resid 2 through 189)FF2 - 18911 - 198
7LYSLYS(chain G and resid 2 through 189)GG2 - 18911 - 198
8LYSLYS(chain H and resid 2 through 189)HH2 - 18911 - 198
9LYSLYS(chain I and resid 2 through 189)II2 - 18911 - 198
10LYSLYS(chain J and resid 2 through 189)JJ2 - 18911 - 198
11HISHISchain KKK-1 - 1898 - 198
12LYSLYSchain LLL2 - 18911 - 198
13LYSLYS(chain M and resid 2 through 189)MM2 - 18911 - 198
14LYSLYS(chain N and resid 2 through 189)NN2 - 18911 - 198
15LYSLYS(chain O and resid 2 through 189)OO2 - 18911 - 198
16LYSLYS(chain P and resid 2 through 189)PP2 - 18911 - 198

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Components

#1: Protein
Aequorin-2


Mass: 22544.117 Da / Num. of mol.: 16 / Fragment: UNP residues 9-196
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-9A3 / (2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one


Mass: 507.461 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C27H20F3N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1402 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10mM Bis-Tris(pH7.3), 2M Ammonium sulfate, 2mM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→46.608 Å / Num. obs: 206078 / % possible obs: 97.6 % / Redundancy: 3.95 % / Biso Wilson estimate: 34.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.101 / Χ2: 0.949 / Net I/σ(I): 12.06 / Num. measured all: 814099
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
2.15-2.283.8830.7622.0112548734082323190.9750.88394.8
2.28-2.433.9810.513.0712414932073311850.8880.5997.2
2.43-2.633.9810.3474.3111611829857291680.9430.40197.7
2.63-2.883.9730.2076.910686327470268940.9750.23997.9
2.88-3.223.9740.11311.359685224792243730.9930.13198.3
3.22-3.713.9520.05720.018539421907216100.9980.06698.6
3.71-4.543.9360.03730.017215418533183300.9980.04398.9
4.54-6.393.9270.03332.575599114368142590.9990.03899.2
6.39-46.6083.9160.02736.631091803779400.9990.03198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.91 Å46.61 Å
Translation8.91 Å46.61 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.6.0phasing
PHENIX(1.11.1_2575: ???)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EJ3

1ej3


Resolution: 2.147→46.608 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 2000 97 %
Rwork0.1961 203733 -
obs0.1964 205733 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.95 Å2 / Biso mean: 42.1773 Å2 / Biso min: 18.78 Å2
Refinement stepCycle: final / Resolution: 2.147→46.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24426 0 592 1402 26420
Biso mean--36.61 43.69 -
Num. residues----3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825703
X-RAY DIFFRACTIONf_angle_d0.91634873
X-RAY DIFFRACTIONf_chiral_restr0.0553501
X-RAY DIFFRACTIONf_plane_restr0.0074520
X-RAY DIFFRACTIONf_dihedral_angle_d14.11114767
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14795X-RAY DIFFRACTION9.939TORSIONAL
12B14795X-RAY DIFFRACTION9.939TORSIONAL
13C14795X-RAY DIFFRACTION9.939TORSIONAL
14D14795X-RAY DIFFRACTION9.939TORSIONAL
15E14795X-RAY DIFFRACTION9.939TORSIONAL
16F14795X-RAY DIFFRACTION9.939TORSIONAL
17G14795X-RAY DIFFRACTION9.939TORSIONAL
18H14795X-RAY DIFFRACTION9.939TORSIONAL
19I14795X-RAY DIFFRACTION9.939TORSIONAL
110J14795X-RAY DIFFRACTION9.939TORSIONAL
111K14795X-RAY DIFFRACTION9.939TORSIONAL
112L14795X-RAY DIFFRACTION9.939TORSIONAL
113M14795X-RAY DIFFRACTION9.939TORSIONAL
114N14795X-RAY DIFFRACTION9.939TORSIONAL
115O14795X-RAY DIFFRACTION9.939TORSIONAL
116P14795X-RAY DIFFRACTION9.939TORSIONAL
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 (%)
2.1473-2.2010.32091350.2877137401387592
2.201-2.26050.36631410.3158143721451396
2.2605-2.3270.32191420.2638145201466297
2.327-2.40220.26191430.2397145211466497
2.4022-2.4880.30461420.2308145761471897
2.488-2.58760.2731440.227145181466298
2.5876-2.70540.231430.217146011474498
2.7054-2.8480.28981420.2081145751471798
2.848-3.02640.25191440.2035147151485998
3.0264-3.260.21951450.1949146641480998
3.26-3.5880.20221440.1845146931483799
3.588-4.10690.19831440.1686147601490499
4.1069-5.17320.181460.1554148111495799
5.1732-46.61920.20781450.179146671481298

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