PDB-4izn: Structure of pcDronpa-A69T mutant

ID or keywords:

Entry

Database: PDB / ID: 4izn

Title

Structure of pcDronpa-A69T mutant

Components

Fluorescent protein Dronpa

Keywords

FLUORESCENT 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

Biological species

Echinophyllia (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

De Zitter, E. / Nguyen Bich, N. / Van Meervelt, L. / Moeyaert, B.

Citation

Journal: 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

Deposition	Jan 30, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 23, 2014	Group: Database references
Revision 1.2	Nov 8, 2023	Group: 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 2.0	Nov 15, 2023	Group: 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 2.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4izn.cif.gz	567.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4izn.ent.gz	466.8 KB	Display	PDB format
PDBx/mmJSON format	4izn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4izn_validation.pdf.gz	564.7 KB	Display	wwPDB validaton report
Full document	4izn_full_validation.pdf.gz	600.3 KB	Display
Data in XML	4izn_validation.xml.gz	110.4 KB	Display
Data in CIF	4izn_validation.cif.gz	150.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iz/4izn ftp://data.pdbj.org/pub/pdb/validation_reports/iz/4izn	HTTPS FTP

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Related structure data

Related structure data	4hq8C 4hq9C 4hqcC 2ie2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3lsa-d 2ie2-2 6nql-1 6nqv-1 4hq9-1 2h8q-1 4hq9-2 3ls3-d 1zux-d 2z6x-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#174 - Jun 2014 GFP-like Proteins similarity (4) #42 - Jun 2003 Green Fluorescent Protein similarity (4)

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

351 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fluorescent protein Dronpa

B: Fluorescent protein Dronpa

C: Fluorescent protein Dronpa

D: Fluorescent protein Dronpa

hetero molecules

defined by author
117 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Fluorescent protein Dronpa

F: Fluorescent protein Dronpa

G: Fluorescent protein Dronpa

H: Fluorescent protein Dronpa

hetero molecules

defined by author
117 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: Fluorescent protein Dronpa

J: Fluorescent protein Dronpa

K: Fluorescent protein Dronpa

L: Fluorescent protein Dronpa

hetero molecules

defined by author
117 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3

#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 modification	Y
Sequence details	RESIDUE CYS 62 MUTATED TO HIS 62. HIS 62, TYR 63 AND GLY 64 CIRCULARIZED INTO ONE CHROMOPHORE, CR8.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.58 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2012
Radiation	Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 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 / B_iso Wilson estimate: 35.32 Å²
Reflection shell	Resolution: 2.15→2.27 Å / Redundancy: 3.2 % / R_merge(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

Name	Version	Classification
PXIII	program	data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2453	8087	5 %	random
R_work	0.1922	-	-	-
all	0.1949	161957	-	-
obs	0.1949	161738	99.65 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 107.38 Å² / B_iso mean: 31.2809 Å² / B_iso min: 5.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→34.803 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20965	0	12	1481	22458

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	21895
X-RAY DIFFRACTION	f_angle_d	1.158	29698
X-RAY DIFFRACTION	f_chiral_restr	0.084	3015
X-RAY DIFFRACTION	f_plane_restr	0.005	3885
X-RAY DIFFRACTION	f_dihedral_angle_d	14.791	8172

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	L	492	X-RAY DIFFRACTION	POSITIONAL
1	2	A	492	X-RAY DIFFRACTION	POSITIONAL	0.044
1	3	B	492	X-RAY DIFFRACTION	POSITIONAL	0.045
1	4	C	491	X-RAY DIFFRACTION	POSITIONAL	0.041
1	5	D	493	X-RAY DIFFRACTION	POSITIONAL	0.038
1	6	E	492	X-RAY DIFFRACTION	POSITIONAL	0.044
1	7	F	492	X-RAY DIFFRACTION	POSITIONAL	0.046
1	8	G	492	X-RAY DIFFRACTION	POSITIONAL	0.045
1	9	H	492	X-RAY DIFFRACTION	POSITIONAL	0.044
1	10	I	492	X-RAY DIFFRACTION	POSITIONAL	0.042
1	11	J	490	X-RAY DIFFRACTION	POSITIONAL	0.044
1	12	K	491	X-RAY DIFFRACTION	POSITIONAL	0.041
2	1	L	226	X-RAY DIFFRACTION	POSITIONAL
2	2	A	226	X-RAY DIFFRACTION	POSITIONAL	0.039
2	3	B	226	X-RAY DIFFRACTION	POSITIONAL	0.042
2	4	C	226	X-RAY DIFFRACTION	POSITIONAL	0.038
2	5	D	226	X-RAY DIFFRACTION	POSITIONAL	0.035
2	6	E	226	X-RAY DIFFRACTION	POSITIONAL	0.038
2	7	F	226	X-RAY DIFFRACTION	POSITIONAL	0.039
2	8	G	226	X-RAY DIFFRACTION	POSITIONAL	0.043
2	9	H	226	X-RAY DIFFRACTION	POSITIONAL	0.04
2	10	I	226	X-RAY DIFFRACTION	POSITIONAL	0.038
2	11	J	226	X-RAY DIFFRACTION	POSITIONAL	0.043
2	12	K	221	X-RAY DIFFRACTION	POSITIONAL	0.036
3	1	L	64	X-RAY DIFFRACTION	POSITIONAL
3	2	A	64	X-RAY DIFFRACTION	POSITIONAL	0.072
3	3	B	64	X-RAY DIFFRACTION	POSITIONAL	0.062
3	4	C	60	X-RAY DIFFRACTION	POSITIONAL	0.057
3	5	D	64	X-RAY DIFFRACTION	POSITIONAL	0.051
3	6	E	64	X-RAY DIFFRACTION	POSITIONAL	0.059
3	7	F	64	X-RAY DIFFRACTION	POSITIONAL	0.058
3	8	G	64	X-RAY DIFFRACTION	POSITIONAL	0.062
3	9	H	64	X-RAY DIFFRACTION	POSITIONAL	0.054
3	10	I	64	X-RAY DIFFRACTION	POSITIONAL	0.064
3	11	J	64	X-RAY DIFFRACTION	POSITIONAL	0.064
3	12	K	64	X-RAY DIFFRACTION	POSITIONAL	0.056

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.15-2.1744	0.3563	284	0.2949	5128	5412	99
2.1744-2.2	0.3279	242	0.2957	5132	5374	99
2.2-2.2268	0.335	256	0.2989	5043	5299	100
2.2268-2.255	0.3678	246	0.2954	5165	5411	100
2.255-2.2847	0.3942	288	0.2976	5053	5341	100
2.2847-2.316	0.3445	268	0.2856	5121	5389	100
2.316-2.3491	0.319	276	0.2662	5133	5409	100
2.3491-2.3841	0.3285	270	0.2665	5085	5355	100
2.3841-2.4214	0.3176	273	0.2589	5141	5414	100
2.4214-2.461	0.315	283	0.2504	5110	5393	100
2.461-2.5035	0.3083	269	0.2564	5109	5378	100
2.5035-2.549	0.3336	284	0.2619	5103	5387	100
2.549-2.598	0.3192	269	0.2448	5100	5369	100
2.598-2.651	0.2974	269	0.2299	5094	5363	100
2.651-2.7086	0.2861	258	0.2292	5153	5411	100
2.7086-2.7716	0.3019	268	0.223	5135	5403	100
2.7716-2.8409	0.3	268	0.225	5129	5397	100
2.8409-2.9177	0.2946	266	0.2236	5141	5407	100
2.9177-3.0035	0.2751	302	0.2079	5073	5375	99
3.0035-3.1004	0.2728	249	0.2174	5117	5366	100
3.1004-3.2111	0.2459	277	0.2134	5120	5397	100
3.2111-3.3396	0.2816	286	0.2082	5098	5384	100
3.3396-3.4914	0.2367	249	0.1949	5122	5371	99
3.4914-3.6753	0.2404	290	0.1785	5081	5371	99
3.6753-3.9053	0.2089	271	0.168	5130	5401	100
3.9053-4.2063	0.2031	242	0.1515	5142	5384	100
4.2063-4.6288	0.1579	235	0.124	5174	5409	100
4.6288-5.2965	0.1694	286	0.1177	5138	5424	100
5.2965-6.6654	0.1768	284	0.1343	5171	5455	100
6.6654-34.8075	0.176	279	0.157	5210	5489	100

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