PDB-3nf0: mPlum-TTN

ID or keywords:

Entry

Database: PDB / ID: 3nf0

Title

mPlum-TTN

Components

Fluorescent protein plum

Keywords

FLUORESCENT PROTEIN / mPlum / mCherry / RFPs

Function / homology

Function and homology information

bioluminescence / generation of precursor metabolites and energy
Similarity search - Function

Biological species

Discosoma sp. LW-2004 (sea anemone)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Mayo, S.L. / Chica, R.A. / Moore, M.M.

Citation

Journal: To be Published
Title: Structural Basis for Changes in the Fluorescent Properties of Computationally Designed Red Fluorescent Proteins
Authors: Moore, M.M. / Chica, R.A. / Mayo, S.L.

History

Deposition	Jun 9, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 13, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3	Sep 6, 2023	Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 22, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3nf0.cif.gz	111 KB	Display	PDBx/mmCIF format
PDB format	pdb3nf0.ent.gz	85.2 KB	Display	PDB format
PDBx/mmJSON format	3nf0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3nf0_validation.pdf.gz	458.2 KB	Display	wwPDB validaton report
Full document	3nf0_full_validation.pdf.gz	472.8 KB	Display
Data in XML	3nf0_validation.xml.gz	15 KB	Display
Data in CIF	3nf0_validation.cif.gz	19.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nf/3nf0 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/3nf0	HTTPS FTP

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Related structure data

Related structure data	2qlgS 3neb PDB Unreleased entry 3nez S: Starting model for refinement
Similar structure data	4zio-2 4kf4-2 6myb-5 4zio-1 5fhv-d 4zin-1 2qlg-2 4dxn-d 4kf4-7 5h89-4 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 (4) #42 - Jun 2003 Green Fluorescent Protein similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: Fluorescent protein plum

hetero molecules

27 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	38.270, 61.300, 94.240
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Fluorescent protein plum Mass: 26580.881 Da / Num. of mol.: 1 / Mutation: I197T, A217N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Gold (DE3) / References: UniProt: Q5S3G7
#2: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₅
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	MET 66, TYR 67, AND GLY 68 CIRCULARIZED INTO ONE CHROMOPHORE

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.85 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.1 M malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 4, 2009
Radiation	Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→37.4 Å / Num. obs: 22906 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / R_merge(I) obs: 0.089 / Net I/σ(I): 7.6
Reflection shell	Resolution: 1.75→1.84 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3288 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QLG CHAIN A, CHROMOPHORE REMOVED, MUTATIONS TRUNCATED.

2qlg

Resolution: 1.75→32.463 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2561	1168	5.11 %
R_work	0.2077	-	-
obs	0.2102	22854	99.11 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.91 Å² / k_sol: 0.481 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4626 Å²	0 Å²	-0 Å²
2-	-	1.6426 Å²	0 Å²
3-	-	-	-1.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→32.463 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1753	0	27	107	1887

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.047	3639
X-RAY DIFFRACTION	f_angle_d	2.614	6578
X-RAY DIFFRACTION	f_dihedral_angle_d	19.076	912
X-RAY DIFFRACTION	f_chiral_restr	0.191	254
X-RAY DIFFRACTION	f_plane_restr	0.014	566

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.75-1.8296	0.3178	142	0.2624	2658	X-RAY DIFFRACTION	100
1.8296-1.9261	0.2992	149	0.2627	2674	X-RAY DIFFRACTION	100
1.9261-2.0467	0.3395	141	0.2392	2703	X-RAY DIFFRACTION	100
2.0467-2.2047	0.3046	150	0.2339	2681	X-RAY DIFFRACTION	100
2.2047-2.4266	0.2784	132	0.2177	2731	X-RAY DIFFRACTION	99
2.4266-2.7775	0.2578	144	0.2075	2683	X-RAY DIFFRACTION	98
2.7775-3.4987	0.2271	151	0.1791	2708	X-RAY DIFFRACTION	97
3.4987-32.4686	0.2049	159	0.1785	2848	X-RAY DIFFRACTION	99

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	0.4019	0.0637	-0.0227	0.0661	0.1456	0.0436	0.0006	-0.0229	0.2195	0.0019	0.1213	-0.1201	-0.057	0.4031	-0.1277	0.053	0.0141	0.0242	0.1406	-0.0083	0.127	25.4588	12.2775	25.0513
2	-0.0759	-0.0376	-0.3592	0.2452	-0.0219	0.5879	0.0288	0.004	-0.0135	-0.3717	-0.1465	0.0614	0.1944	0.0289	0.0835	0.4939	-0.0259	0.0122	0.0864	-0.0064	0.0963	21.5242	9.8662	0.7285
3	0.2277	-0.1654	-0.0254	-0.2123	0.1967	1.6872	-0.0789	0.0428	0.0875	-0.4647	0.0421	-0.0218	-0.1556	-0.0402	0.0085	0.377	-0.0399	0.0497	0.0787	0.0188	0.098	24.2424	14.7966	4.6565
4	-1.5912	0.0971	-1.3457	1.1829	-0.7064	0.9164	0.0408	-0.0658	0.3849	-0.076	0.1752	0.16	0.0255	-0.1661	-0.1974	0.0033	0.0036	-0.0133	0.1327	-0.0098	0.1695	17.5015	15.6487	25.0623
5	0.0473	-0.1893	-0.066	0.9267	0.9148	-0.0144	0.1327	0.0067	0.0776	-0.4896	0.0938	-0.1759	0.0938	0.0656	-0.2004	0.6146	-0.0244	0.0289	0.04	0.0155	0.0729	24.3121	19.5962	4.0396
6	1.3413	-0.7138	-0.4119	6.1595	2.6952	-0.6114	0.0251	-0.147	-0.0531	-1.0949	-0.2117	0.1213	0.0212	-0.0297	0.0746	-0.0132	0.0318	-0.0639	0.0047	-0.0121	0.0536	14.8793	13.2223	10.0679
7	-0.2834	1.0224	0.3086	-0.0971	-0.756	0.8232	-0.0419	-0.1064	0.2135	0.0448	0.1082	0.0283	0.1692	-0.1956	-0.0833	0.0502	0.0066	0.003	0.0956	-0.0149	0.1546	16.9608	1.875	25.4007
8	-0.2961	-0.1625	-0.4406	1.6025	1.2382	0.8183	-0.0091	0.0359	-0.1839	-0.7494	0.0107	0.1908	-0.4877	0.0958	0.007	0.3063	0.0378	-0.1124	0.0725	-0.03	0.0988	9.7484	4.744	3.6591
9	0.4275	0.7683	-0.341	1.6975	0.6341	0.2613	0.111	-0.3756	-0.151	-0.0714	0.0362	-0.4328	-0.0165	0.1043	-0.1554	-0.0128	0.0016	0.0177	0.1334	-0.0218	0.1023	25.4605	4.6106	15.0078
10	0.9294	0.7074	-0.5291	3.2197	-0.1791	0.9262	-0.0424	-0.0049	0.0436	-0.7025	-0.2114	-0.1648	0.1581	0.1226	0.256	0.1841	0.0276	0.0624	0.0751	0.0178	0.1106	25.3471	7.7251	13.3462
11	0.1572	0.633	-0.1714	-1.3219	-0.346	0.2173	-0.1171	0.0108	-0.1554	-0.3599	0.0264	0.1715	0.1178	0.0002	0.0825	0.6611	-0.0897	-0.1039	0.0274	-0.013	0.1436	13.948	5.8424	-3.7941
12	0.354	0.113	0.2422	-1.3494	0.6278	1.0848	-0.1924	0.0821	0.1365	0.2809	0.102	-0.228	-0.3483	-0.1244	0.0759	0.9527	0.0606	-0.2847	0.0368	0.0021	0.1225	7.7317	17.2944	-6.0991
13	0.0494	0.0039	0.1377	1.8657	-0.3625	-0.3851	-0.1064	-0.0089	-0.1279	-0.6263	-0.2233	0.0661	-0.4157	-0.0518	0.3306	0.4204	0.1006	-0.1988	0.1417	-0.0371	0.2336	4.4922	17.8626	9.6108
14	-3.0036	-0.1572	-0.4961	0.49	0.6072	0.939	-0.0745	0.0297	0.128	-0.0264	-0.3812	0.3669	0.0678	-0.3339	0.4077	0.0475	-0.0007	-0.0387	0.1591	-0.0525	0.305	5.3995	-1.4294	17.3208
15	2.02	0.9335	0.546	-0.1512	0.9291	1.7381	-0.1615	-0.2158	-0.0149	-0.1873	-0.0597	0.0355	-0.3519	-0.1547	0.2143	0.068	0.0552	-0.06	0.0497	-0.0447	0.057	5.9894	2.0917	13.5446
16	1.6439	2.2488	-0.1389	-3.5528	1.3851	0.8602	-0.1475	-0.0898	0.5695	-0.5921	0.1273	0.7395	0.0201	0.1133	0.0229	0.6062	0.0417	-0.2398	0.1598	-0.0157	0.3359	0.6513	17.3186	3.4517
17	1.4781	-0.0624	1.1934	-0.6243	0.1907	1.0323	0.0465	-0.065	-0.2902	-0.0707	0.1094	0.15	-0.1848	-0.0707	-0.1483	0.1307	-0.0129	-0.0186	0.0619	0.0067	0.1308	14.4731	-1.6542	14.5363
18	0.3366	-1.0284	0.8114	1.4953	-0.0094	1.0836	-0.0695	-0.2853	-0.0561	0.001	-0.0187	-0.0398	-0.1679	-0.1858	0.0784	0.0119	0.0135	-0.0007	0.1298	-0.0184	0.1918	8.9853	5.1503	21.5038
19	-0.0173	0.9337	0.9136	1.9194	0.0668	2.7215	-0.2619	0.0438	0.0001	-1.2784	-0.0531	0.2768	-0.8747	0.0734	0.3046	0.7608	0.053	-0.0711	0.0737	0.0072	0.09	18.0857	25.1497	7.1168
20	3.1068	0.1539	1.3376	0.6315	0.5944	1.977	-0.1343	-0.407	-0.3467	-0.0583	-0.1048	0.1402	-0.158	-0.6301	0.2493	0.0824	0.0351	-0.0053	0.217	-0.0401	0.1833	4.23	9.3546	24.025

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 6:15)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 16:24)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 25:34)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 35:43)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 44:53)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 54:74)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 75:91)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 92:106)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 107:116)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 117:123)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 124:128)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 129:140)
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 141:146)
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 147:154)
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 155:163)
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 164:176)
17	X-RAY DIFFRACTION	17	(CHAIN A AND RESID 177:185)
18	X-RAY DIFFRACTION	18	(CHAIN A AND RESID 186:200)
19	X-RAY DIFFRACTION	19	(CHAIN A AND RESID 201:214)
20	X-RAY DIFFRACTION	20	(CHAIN A AND RESID 215:225)

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