PDB-3vic: Green-fluorescent variant of the non-fluorescent chromoprotein Rtms5

ID or keywords:

Entry

Database: PDB / ID: 3vic

Title

Green-fluorescent variant of the non-fluorescent chromoprotein Rtms5

Components

GFP-like non-fluorescent chromoprotein

Keywords

FLUORESCENT PROTEIN /

Beta Barrel / Beta Can / GFP / Pocilloporin /

Chromoprotein /

Pigment /

Fluorescent /

Anthozoa / Acylimine / Peptide-derived chromophore

Function / homology

Function and homology information

bioluminescence
Similarity search - Function

Biological species

Montipora efflorescens (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Battad, J.M. / Traore, D.A.K. / Byres, E. / Wilce, M. / Devenish, R.J. / Rossjohn, J. / Prescott, M.

Citation

Journal: Plos One / Year: 2012
Title: A Green Fluorescent Protein Containing a QFG Tri-Peptide Chromophore: Optical Properties and X-Ray Crystal Structure.
Authors: Battad, J.M. / Traore, D.A. / Byres, E. / Rossjohn, J. / Devenish, R.J. / Olsen, S. / Wilce, M.C. / Prescott, M.

History

Deposition	Sep 28, 2011	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2012	Group: Database references
Revision 1.2	Nov 2, 2016	Group: Derived calculations / Structure summary
Revision 1.3	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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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 / _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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3vic.cif.gz	761.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3vic.ent.gz	632.9 KB	Display	PDB format
PDBx/mmJSON format	3vic.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vi/3vic ftp://data.pdbj.org/pub/pdb/validation_reports/vi/3vic	HTTPS FTP

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Related structure data

Related structure data	3vk1C 1mouS 1mov 2arl 2p4m S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2p4m-1 6nqp-2 3vk1-1 6nqk-2 1zux-d 2h8q-2 6nqv-1 2h8q-1 1zgq-1 2btj-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#174 - Jun 2014 GFP-like Proteins similarity (3) #42 - Jun 2003 Green Fluorescent Protein similarity (3)

Deposited unit

A: GFP-like non-fluorescent chromoprotein

B: GFP-like non-fluorescent chromoprotein

C: GFP-like non-fluorescent chromoprotein

D: GFP-like non-fluorescent chromoprotein

E: GFP-like non-fluorescent chromoprotein

F: GFP-like non-fluorescent chromoprotein

G: GFP-like non-fluorescent chromoprotein

H: GFP-like non-fluorescent chromoprotein

hetero molecules

219 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GFP-like non-fluorescent chromoprotein

B: GFP-like non-fluorescent chromoprotein

C: GFP-like non-fluorescent chromoprotein

D: GFP-like non-fluorescent chromoprotein

hetero molecules

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

2

E: GFP-like non-fluorescent chromoprotein

F: GFP-like non-fluorescent chromoprotein

G: GFP-like non-fluorescent chromoprotein

H: GFP-like non-fluorescent chromoprotein

hetero molecules

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

Unit cell

Length a, b, c (Å)	150.271, 186.060, 185.150
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 6 / Auth seq-ID: 8 - 223 / Label seq-ID: 23 - 236

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H

#1: Protein	GFP-like non-fluorescent chromoprotein / Non-fluorescent pocilloporin / Rtms 5 Mass: 27126.717 Da / Num. of mol.: 8 / Mutation: Y67F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Montipora efflorescens (invertebrata) / Plasmid: pQE9BN / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: P83690
#2: Chemical	ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1443 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUE TYR 67 HAS BEEN MUTATED TO PHE 67. RESIDUES GLN 66, PHE 67 AND GLY 68 CONSTITUTE THE ...RESIDUE TYR 67 HAS BEEN MUTATED TO PHE 67. RESIDUES GLN 66, PHE 67 AND GLY 68 CONSTITUTE THE CHROMOPHORE QFG 66.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 22% PEG 3350, 0.34M POTASSIUM IODIDE, 0.2M TRIS, PH 8.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2006
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→117.04 Å / Num. obs: 130290

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0110	refinement
HKL-2000		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOU

1mou

Resolution: 2.2→54.8 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.943 / SU B: 9.161 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20447	6587	5 %	RANDOM
R_work	0.15964	-	-	-
obs	0.16189	124333	99.97 %	-
all	-	130290	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 32.179 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.41 Å²	0 Å²	0 Å²
2-	-	-1.9 Å²	0 Å²
3-	-	-	-0.51 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→54.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13975	0	24	1443	15442

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	14534
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.022	1.964	19679
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.357	5	1765
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.87	24.436	647
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15	15	2379
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.69	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	2007
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	11280
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.717	3	8791
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.547	5	14241
X-RAY DIFFRACTION	r_scbond_it	3.721	7	5743
X-RAY DIFFRACTION	r_scangle_it	4.366	10	5432
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1688 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	loose positional	0.24	5
B	loose positional	0.19	5
C	loose positional	0.2	5
D	loose positional	0.24	5
E	loose positional	0.21	5
F	loose positional	0.23	5
G	loose positional	0.22	5
H	loose positional	0.24	5
A	loose thermal	1.41	10
B	loose thermal	1.31	10
C	loose thermal	1.44	10
D	loose thermal	1.33	10
E	loose thermal	1.4	10
F	loose thermal	1.31	10
G	loose thermal	1.39	10
H	loose thermal	1.46	10

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	512	-
R_work	0.221	9125	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.3238	-0.0041	-0.4376	1.4313	-0.2812	2.1482	-0.0486	0.0442	0.2326	0.0071	-0.0165	0.2162	-0.179	-0.2095	0.0652	0.2783	0.0391	-0.049	0.2045	-0.0139	0.3054	-51.664	14.3118	-47.807
2	1.2982	-0.0774	0.4291	1.5333	-0.3633	2.1706	-0.0186	-0.0959	-0.2271	-0.0249	0.0169	0.2394	0.1982	-0.2162	0.0018	0.2505	-0.0336	0.0374	0.2061	0.0055	0.2845	-51.4328	-17.111	-44.0005
3	1.4752	-0.1801	-0.3156	1.6557	0.3795	2.0902	-0.0524	-0.0307	0.3154	-0.0239	0.045	-0.2584	-0.1982	0.2391	0.0074	0.2678	-0.0519	-0.0372	0.2163	0.0087	0.3086	-21.1928	14.8197	-43.704
4	1.3141	0.1192	0.5328	1.3097	0.4244	2.0396	-0.0271	0.0704	-0.2083	0.0094	0.0309	-0.2067	0.1617	0.236	-0.0038	0.2385	0.0428	0.033	0.2201	0.0081	0.2713	-20.7128	-16.8729	-45.4372
5	1.3136	0.5465	-0.1013	2.0952	-0.4095	1.4727	-0.0521	-0.2244	-0.0653	0.1182	0.0546	-0.2007	0.0231	0.1932	-0.0025	0.2364	0.049	-0.0343	0.2579	-0.0225	0.2285	-58.403	43.8991	-76.687
6	1.403	-0.6352	0.0756	1.9676	-0.323	1.4243	-0.0067	0.2382	0.0722	-0.2006	0.0103	-0.1621	0.0229	0.1616	-0.0036	0.2812	-0.0418	0.0365	0.2497	-0.0106	0.2201	-59.7099	47.9004	-108.005
7	1.412	-0.3844	-0.1327	1.9557	0.4524	1.6806	-0.0491	0.2808	-0.0449	-0.2337	0.0167	0.2337	-0.0505	-0.3118	0.0324	0.2859	-0.0372	-0.0647	0.2972	0.0005	0.2413	-90.3238	45.3119	-106.7449
8	1.5583	0.5607	0.0246	2.0358	0.4146	1.6952	-0.0465	-0.244	0.0529	0.1451	0.0483	0.23	0.0486	-0.2141	-0.0018	0.2415	0.0349	0.0207	0.2549	0.0086	0.2361	-89.0039	46.981	-75.1021
9	4.2127	-3.0277	-3.0146	14.1093	14.148	14.187	0.0376	0.1135	0.0828	-0.1517	-0.0245	-0.0087	-0.1555	-0.0184	-0.0131	0.4055	0.0562	0.0547	0.3167	-0.0658	0.3085	-16.6179	-30.3897	-61.1697
10	1.8233	-0.9594	1.0558	10.5344	-10.6266	10.7241	0.2043	0.3731	-0.4946	-0.206	-0.0597	0.1165	0.2181	0.0766	-0.1446	0.4286	0.0818	-0.0785	0.3238	0.0457	0.33	-54.7129	27.197	-64.1872
11	4.9024	2.4216	1.3144	10.5346	8.971	7.7683	0.0211	-0.1715	-0.2059	0.1109	-0.0209	-0.0394	0.1039	0.0093	-0.0002	0.464	-0.0638	-0.0928	0.2885	-0.0551	0.3442	-18.5265	28.6191	-28.0384
12	0.0771	0.0149	0.0417	0.0655	0.0155	0.0676	-0.0218	0.0115	-0.0667	-0.0243	-0.0368	0.0814	0.0395	-0.0112	0.0586	0.3627	-0.0259	0.0453	0.3429	-0.0058	0.3838	-76.7186	2.2347	-73.9461
13	0.2619	0.0282	0.31	0.0051	0.0313	0.371	0.0189	0.0029	-0.0321	-0.0256	0.0084	0.0029	0.055	-0.0016	-0.0273	0.4215	0.0094	-0.0432	0.3466	0.004	0.1422	-36.1909	-7.49	-45.0433
14	0.4477	-0.2538	0.2513	0.1617	-0.1494	0.1536	0.0128	0.0127	0.0094	0.0327	-0.0277	0.0695	-0.0269	0.0652	0.0149	0.3466	0.03	0.0516	0.3763	-0.0009	0.4201	-54.8309	15.4946	-74.9511
15	0.0258	-0.0351	0.0216	0.0756	-0.0556	0.0435	-0.0035	-0.0305	0.0555	0.0186	0.0054	-0.0298	-0.0052	-0.0024	-0.0018	0.3529	-0.0222	0.0471	0.3637	-0.0083	0.2378	-55.9145	16.1772	-62.9572
16	2.4305	0.1439	1.4778	0.0401	0.097	0.9022	-0.1659	0.0478	0.0244	-0.0612	0.1284	0.0208	-0.1405	0.0544	0.0375	0.3277	-0.047	-0.0752	0.435	0.01	0.3365	-74.0155	65.7483	-90.7401
17	1.1639	-0.8429	0.8154	0.6567	-0.6371	0.6559	-0.2491	-0.2125	0.1648	0.3075	0.1369	0.0008	-0.3486	0.0349	0.1122	0.3701	-0.142	0.031	0.6116	-0.1093	0.5606	-54.9289	21.1445	-69.6497
18	0.2418	-0.1878	0.1693	0.1657	-0.1659	0.2286	0.0117	-0.1072	0.1086	-0.0661	0.058	-0.0201	0.005	0.0364	-0.0696	0.362	-0.027	-0.0684	0.3892	-0.0571	0.3227	-55.8705	21.8616	-68.0927
19	0.2559	0.0258	0.4531	0.0057	0.0508	0.8501	0.1952	-0.0498	-0.1721	0.0193	0.0692	-0.0198	0.4418	-0.0131	-0.2644	0.6888	0.0515	-0.0735	0.5145	0.0059	0.1199	-36.2299	-11.7824	-44.8458
20	3.1758	0.0743	4.439	1.5173	0.0787	6.2066	-0.1088	-0.0799	0.1418	0.0868	-0.0605	0.2872	-0.1428	-0.0969	0.1694	0.2075	0.0126	-0.1422	0.3657	-0.0166	0.5825	-74.087	58.7458	-91.0186

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 223
2	X-RAY DIFFRACTION	2	B	8 - 223
3	X-RAY DIFFRACTION	3	C	8 - 223
4	X-RAY DIFFRACTION	4	D	8 - 223
5	X-RAY DIFFRACTION	5	E	8 - 223
6	X-RAY DIFFRACTION	6	F	8 - 223
7	X-RAY DIFFRACTION	7	H	8 - 223
8	X-RAY DIFFRACTION	8	G	8 - 223
9	X-RAY DIFFRACTION	9	D	226 - 227
10	X-RAY DIFFRACTION	10	A	226
11	X-RAY DIFFRACTION	10	E	226
12	X-RAY DIFFRACTION	11	C	226 - 227
13	X-RAY DIFFRACTION	12	H	226
14	X-RAY DIFFRACTION	12	B	226
15	X-RAY DIFFRACTION	13	B	227
16	X-RAY DIFFRACTION	13	D	228
17	X-RAY DIFFRACTION	14	C	228
18	X-RAY DIFFRACTION	14	G	226
19	X-RAY DIFFRACTION	15	A	227
20	X-RAY DIFFRACTION	15	F	226
21	X-RAY DIFFRACTION	16	H	227
22	X-RAY DIFFRACTION	16	E	227
23	X-RAY DIFFRACTION	17	A	228
24	X-RAY DIFFRACTION	17	E	228
25	X-RAY DIFFRACTION	18	H	228
26	X-RAY DIFFRACTION	18	C	229
27	X-RAY DIFFRACTION	19	B	228
28	X-RAY DIFFRACTION	19	D	229
29	X-RAY DIFFRACTION	20	G	227
30	X-RAY DIFFRACTION	20	F	227

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