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- PDB-4izn: Structure of pcDronpa-A69T mutant -

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Basic information

Entry
Database: PDB / ID: 4izn
TitleStructure of pcDronpa-A69T mutant
ComponentsFluorescent protein Dronpa
KeywordsFLUORESCENT PROTEIN / beta barrel / Dronpa
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding / identical protein binding
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDe Zitter, E. / Nguyen Bich, N. / Van Meervelt, L. / Moeyaert, B.
CitationJournal: ACS Nano / Year: 2014
Title: Green-to-red photoconvertible Dronpa mutant for multimodal super-resolution fluorescence microscopy
Authors: Moeyaert, B. / Nguyen Bich, N. / De Zitter, E. / Rocha, S. / Clays, K. / Mizuno, H. / van Meervelt, L. / Hofkens, J. / Dedecker, P.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 3.0Mar 18, 2026Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa
G: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa
I: Fluorescent protein Dronpa
J: Fluorescent protein Dronpa
K: Fluorescent protein Dronpa
L: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,64024
Polymers350,17112
Non-polymers46912
Water26,6801481
1
A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8808
Polymers116,7244
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa
G: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8808
Polymers116,7244
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Fluorescent protein Dronpa
J: Fluorescent protein Dronpa
K: Fluorescent protein Dronpa
L: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8808
Polymers116,7244
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.700, 180.930, 113.161
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
12
22
32
42
52
62
72
82
92
102
112
122
13
23
33
43
53
63
73
83
93
103
113
123

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN L AND (RESID 8:18 OR RESID 21:32 OR RESID...
211CHAIN A AND (RESID 8:18 OR RESID 21:32 OR RESID...
311CHAIN B AND (RESID 8:18 OR RESID 21:32 OR RESID...
411CHAIN C AND (RESID 8:18 OR RESID 21:32 OR RESID...
511CHAIN D AND (RESID 8:18 OR RESID 21:32 OR RESID...
611CHAIN E AND (RESID 8:18 OR RESID 21:32 OR RESID...
711CHAIN F AND (RESID 8:18 OR RESID 21:32 OR RESID...
811CHAIN G AND (RESID 8:18 OR RESID 21:32 OR RESID...
911CHAIN H AND (RESID 8:18 OR RESID 21:32 OR RESID...
1011CHAIN I AND (RESID 8:18 OR RESID 21:32 OR RESID...
1111CHAIN J AND (RESID 8:18 OR RESID 21:32 OR RESID...
1211CHAIN K AND (RESID 8:18 OR RESID 21:32 OR RESID...
112CHAIN L AND (RESID 10 OR RESID 12 OR RESID...
212CHAIN A AND (RESID 10 OR RESID 12 OR RESID...
312CHAIN B AND (RESID 10 OR RESID 12 OR RESID...
412CHAIN C AND (RESID 10 OR RESID 12 OR RESID...
512CHAIN D AND (RESID 10 OR RESID 12 OR RESID...
612CHAIN E AND (RESID 10 OR RESID 12 OR RESID...
712CHAIN F AND (RESID 10 OR RESID 12 OR RESID...
812CHAIN G AND (RESID 10 OR RESID 12 OR RESID...
912CHAIN H AND (RESID 10 OR RESID 12 OR RESID...
1012CHAIN I AND (RESID 10 OR RESID 12 OR RESID...
1112CHAIN J AND (RESID 10 OR RESID 12 OR RESID...
1212CHAIN K AND (RESID 10 OR RESID 12 OR RESID...
113CHAIN L AND (RESID 17 OR RESID 90 OR RESID...
213CHAIN A AND (RESID 17 OR RESID 90 OR RESID...
313CHAIN B AND (RESID 17 OR RESID 90 OR RESID...
413CHAIN C AND (RESID 17 OR RESID 90 OR RESID...
513CHAIN D AND (RESID 17 OR RESID 90 OR RESID...
613CHAIN E AND (RESID 17 OR RESID 90 OR RESID...
713CHAIN F AND (RESID 17 OR RESID 90 OR RESID...
813CHAIN G AND (RESID 17 OR RESID 90 OR RESID...
913CHAIN H AND (RESID 17 OR RESID 90 OR RESID...
1013CHAIN I AND (RESID 17 OR RESID 90 OR RESID...
1113CHAIN J AND (RESID 17 OR RESID 90 OR RESID...
1213CHAIN K AND (RESID 17 OR RESID 90 OR RESID...

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Fluorescent protein Dronpa


Mass: 29180.912 Da / Num. of mol.: 12 / Mutation: V60A, C62H, A69T, N94S, N102I, E218G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia (invertebrata) / Strain: SC22 / Gene: Dronpa / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TLG6
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1481 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE CYS 62 MUTATED TO HIS 62. HIS 62, TYR 63 AND GLY 64 CIRCULARIZED INTO ONE CHROMOPHORE, CR8.

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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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M KCl, 0.05M HEPES, 32%(v/v) PEP 426, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2012
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→34.803 Å / Num. all: 161957 / Num. obs: 161957 / % possible obs: 99.7 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Biso Wilson estimate: 35.32 Å2
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 1.5 / Num. unique all: 23611 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PXIIIprogramdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IE2

2ie2


Resolution: 2.15→34.803 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.78 / SU ML: 0.32 / σ(F): 1.33 / Phase error: 28.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 8087 5 %random
Rwork0.1922 ---
all0.1949 161957 --
obs0.1949 161738 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.38 Å2 / Biso mean: 31.2809 Å2 / Biso min: 5.44 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20965 0 12 1481 22458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821895
X-RAY DIFFRACTIONf_angle_d1.15829698
X-RAY DIFFRACTIONf_chiral_restr0.0843015
X-RAY DIFFRACTIONf_plane_restr0.0053885
X-RAY DIFFRACTIONf_dihedral_angle_d14.7918172
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L492X-RAY DIFFRACTIONPOSITIONAL
12A492X-RAY DIFFRACTIONPOSITIONAL0.044
13B492X-RAY DIFFRACTIONPOSITIONAL0.045
14C491X-RAY DIFFRACTIONPOSITIONAL0.041
15D493X-RAY DIFFRACTIONPOSITIONAL0.038
16E492X-RAY DIFFRACTIONPOSITIONAL0.044
17F492X-RAY DIFFRACTIONPOSITIONAL0.046
18G492X-RAY DIFFRACTIONPOSITIONAL0.045
19H492X-RAY DIFFRACTIONPOSITIONAL0.044
110I492X-RAY DIFFRACTIONPOSITIONAL0.042
111J490X-RAY DIFFRACTIONPOSITIONAL0.044
112K491X-RAY DIFFRACTIONPOSITIONAL0.041
21L226X-RAY DIFFRACTIONPOSITIONAL
22A226X-RAY DIFFRACTIONPOSITIONAL0.039
23B226X-RAY DIFFRACTIONPOSITIONAL0.042
24C226X-RAY DIFFRACTIONPOSITIONAL0.038
25D226X-RAY DIFFRACTIONPOSITIONAL0.035
26E226X-RAY DIFFRACTIONPOSITIONAL0.038
27F226X-RAY DIFFRACTIONPOSITIONAL0.039
28G226X-RAY DIFFRACTIONPOSITIONAL0.043
29H226X-RAY DIFFRACTIONPOSITIONAL0.04
210I226X-RAY DIFFRACTIONPOSITIONAL0.038
211J226X-RAY DIFFRACTIONPOSITIONAL0.043
212K221X-RAY DIFFRACTIONPOSITIONAL0.036
31L64X-RAY DIFFRACTIONPOSITIONAL
32A64X-RAY DIFFRACTIONPOSITIONAL0.072
33B64X-RAY DIFFRACTIONPOSITIONAL0.062
34C60X-RAY DIFFRACTIONPOSITIONAL0.057
35D64X-RAY DIFFRACTIONPOSITIONAL0.051
36E64X-RAY DIFFRACTIONPOSITIONAL0.059
37F64X-RAY DIFFRACTIONPOSITIONAL0.058
38G64X-RAY DIFFRACTIONPOSITIONAL0.062
39H64X-RAY DIFFRACTIONPOSITIONAL0.054
310I64X-RAY DIFFRACTIONPOSITIONAL0.064
311J64X-RAY DIFFRACTIONPOSITIONAL0.064
312K64X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.17440.35632840.29495128541299
2.1744-2.20.32792420.29575132537499
2.2-2.22680.3352560.298950435299100
2.2268-2.2550.36782460.295451655411100
2.255-2.28470.39422880.297650535341100
2.2847-2.3160.34452680.285651215389100
2.316-2.34910.3192760.266251335409100
2.3491-2.38410.32852700.266550855355100
2.3841-2.42140.31762730.258951415414100
2.4214-2.4610.3152830.250451105393100
2.461-2.50350.30832690.256451095378100
2.5035-2.5490.33362840.261951035387100
2.549-2.5980.31922690.244851005369100
2.598-2.6510.29742690.229950945363100
2.651-2.70860.28612580.229251535411100
2.7086-2.77160.30192680.22351355403100
2.7716-2.84090.32680.22551295397100
2.8409-2.91770.29462660.223651415407100
2.9177-3.00350.27513020.20795073537599
3.0035-3.10040.27282490.217451175366100
3.1004-3.21110.24592770.213451205397100
3.2111-3.33960.28162860.208250985384100
3.3396-3.49140.23672490.19495122537199
3.4914-3.67530.24042900.17855081537199
3.6753-3.90530.20892710.16851305401100
3.9053-4.20630.20312420.151551425384100
4.2063-4.62880.15792350.12451745409100
4.6288-5.29650.16942860.117751385424100
5.2965-6.66540.17682840.134351715455100
6.6654-34.80750.1762790.15752105489100

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