PDB-4h3n: mPlumAYC

ID or keywords:

Entry

Database: PDB / ID: 4h3n

Title

mPlumAYC

Components

Fluorescent protein plum

Fluorescence

Keywords

FLUORESCENT PROTEIN

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

Moore, M.M. / Chica, R.A.

Citation

Journal: Plos One / Year: 2012
Title: Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design.
Authors: Moore, M.M. / Oteng-Pabi, S.K. / Pandelieva, A.T. / Mayo, S.L. / Chica, R.A.

History

Deposition	Sep 14, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 24, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 16, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 20, 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_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	Dec 6, 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	4h3n.cif.gz	102.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4h3n.ent.gz	78.3 KB	Display	PDB format
PDBx/mmJSON format	4h3n.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/h3/4h3n ftp://data.pdbj.org/pub/pdb/validation_reports/h3/4h3n	HTTPS FTP

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Related structure data

Related structure data	4h3lC 4h3mC 2qlgS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4kf4-7 4kf4-2 4h3l-1 3kct-d 4zin-1 4h3l-2 4kf4-1 4tza-2 5hzt-10 4zio-3 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)

Deposited unit

A: Fluorescent protein plum

hetero molecules

26.6 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)	38.720, 61.550, 96.290
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 / Fluorescence / mPlumAYC Mass: 26599.949 Da / Num. of mol.: 1 / Mutation: T195A,I197Y,A217C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S3G7
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	MET66, TYR67, AND GLY68 CIRCULARIZED INTO ONE CHROMOPHORE (NRQ).

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 42.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.3 uL + 0.3 uL drops, precipitant: 200 mM sodium cacodylate, 100 mM Tris-HCl, pH 8.5, 30% (w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 90 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1.5418, 1.5621, 1.7321

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2012

Radiation

Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	1.5621	1
3	1.7321	1

Reflection

Resolution: 1.75→37.92 Å / Num. obs: 22710 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QLG

2qlg

Resolution: 1.75→37.92 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.876 / SU B: 7.129 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28104	1168	5.1 %	RANDOM
R_work	0.22126	-	-	-
obs	0.22434	21540	94.72 %	-

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: 16.296 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.03 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	-0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→37.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1687	0	1	103	1791

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.021	1737
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1182
X-RAY DIFFRACTION	r_angle_refined_deg	1.999	1.967	2340
X-RAY DIFFRACTION	r_angle_other_deg	2.263	3	2866
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.429	5	212
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.134	24.198	81
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.053	15	278
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.749	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.138	0.2	238
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	1948
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	357
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	0.948	1.5	1059
X-RAY DIFFRACTION	r_mcbond_other	0.349	1.5	435
X-RAY DIFFRACTION	r_mcangle_it	1.394	2	1690
X-RAY DIFFRACTION	r_scbond_it	2.458	3	678
X-RAY DIFFRACTION	r_scangle_it	3.613	4.5	649
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.75→1.795 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	95	-
R_work	0.265	1618	-
obs	-	-	99.71 %

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	4.7957	1.9052	-0.6878	12.7509	0.5822	-0.6803	-0.1792	-0.2377	-0.3637	0.3574	0.2755	-0.5147	0.0222	0.0764	-0.0963	0.0584	0.0113	-0.0563	0.1326	0.0004	0.0863	25.2083	11.9086	29.3144
2	0.6787	0.7783	1.2316	1.6586	1.0507	3.5781	-0.0934	0.1652	-0.0241	-0.2632	0.1076	-0.1347	0.0912	0.1422	-0.0142	0.1129	0.0204	0.0098	0.1181	-0.0021	0.0713	23.1543	11.5016	6.4654
3	-0.0651	0.3801	-0.5149	1.4125	2.4763	14.1935	-0.0594	0.0538	-0.0096	-0.272	0.0895	-0.39	-0.0132	0.1297	-0.0301	0.1123	0.0073	0.0115	0.0995	0.0031	0.1019	25.1139	15.3049	8.3424
4	3.6158	0.9875	-0.1771	4.8955	-4.4689	5.9705	-0.1134	-0.1447	0.0028	0.1776	0.1716	0.0524	-0.0716	-0.0785	-0.0582	0.0417	0.0236	-0.0279	0.0775	-0.0039	0.0703	17.5981	14.61	27.5423
5	1.8184	0.3507	-1.249	2.6589	-0.3943	3.5427	-0.0676	0.1642	0.1142	-0.3749	0.0503	-0.0219	-0.1133	0.1279	0.0174	0.0648	-0.0094	-0.017	0.091	0.0316	0.0661	22.8902	19.1547	7.677
6	0.6539	-0.0955	0.6429	3.2842	-2.3784	4.3209	-0.0539	0.135	0.0541	-0.2955	-0.0316	0.05	0.1428	0.1319	0.0856	0.0288	-0.0154	-0.0213	0.1265	0.0058	0.0814	14.7375	13.3229	7.5713
7	3.0428	0.0678	-1.4718	0.2291	0.4189	0.8376	0.0023	-0.1395	0.09	0.1727	0.0224	0.1391	-0.0237	0.0301	-0.0247	0.0726	0.0048	0.007	0.1159	0.019	0.0734	13.1922	4.5789	27.7255
8	1.5532	0.2625	0.7526	1.1714	-0.5718	1.7221	0.0922	0.1098	-0.0446	-0.1399	-0.06	-0.1812	0.107	0.147	-0.0322	0.0347	0.0111	0	0.0984	-0.0082	0.0805	19.5583	0.647	17.071
9	4.3558	0.7057	-1.309	3.7054	-0.4819	2.9821	-0.2084	0.1688	-0.3688	-0.3073	0.1566	0.2402	0.0684	-0.2819	0.0518	0.1597	0.0026	-0.0471	0.161	0.0048	0.0662	5.0073	7.1037	0.2482
10	4.8693	3.8919	5.1272	3.7011	3.1903	8.2477	0.1112	0.2013	-0.2698	-0.0594	0.1165	-0.3424	-0.0478	0.3456	-0.2277	0.1068	0.0222	0.0132	0.0698	-0.0127	0.0987	23.5184	3.3121	13.1833
11	3.0463	0.3084	3.0942	1.3241	0.0452	5.066	-0.0138	0.2093	-0.1202	-0.1622	0.1224	-0.2224	0.0831	0.1779	-0.1086	0.0388	0.0071	0.0377	0.0842	0.0091	0.0802	22.9434	7.1717	10.389
12	1.5818	1.5704	-0.0878	16.0938	9.4227	7.0628	-0.0991	0.3312	0.1976	-0.3747	0.126	0.2601	-0.1621	-0.1075	-0.027	0.1847	-0.0344	-0.0784	0.1789	0.0599	0.0332	7.1068	16.4489	-5.2803
13	6.4134	0.7	-1.2348	-2.106	-0.4424	12.2472	-0.0475	-0.0588	-0.1583	0.0962	-0.0023	0.0832	-0.1641	-0.3184	0.0499	0.0446	0.0244	-0.0451	0.0902	0.0239	0.1156	4.6476	17.2157	10.1721
14	1.9637	-4.0956	1.1351	8.7232	-3.3841	2.1456	0.0356	-0.011	-0.2825	-0.3783	0.1966	0.7152	0.0861	-0.1046	-0.2322	0.0177	-0.0085	-0.0522	0.1333	0.0076	0.164	6.2433	-2.4339	17.6992
15	1.6205	1.6554	-0.8859	5.8698	1.0217	0.4918	0.1386	0.1306	0.2719	-0.1423	-0.1509	0.4674	-0.036	-0.1091	0.0123	0.0909	0.0168	-0.0552	0.177	0.0394	0.1231	1.186	14.8813	6.0082
16	13.3149	4.3957	5.7197	0.5904	-0.5103	6.9201	0.1386	-0.1842	-0.7698	0.0879	0.2746	0.1832	0.1865	-0.4605	-0.4132	0.076	0.0024	-0.0107	0.0956	0.0221	0.1292	11.7689	-1.5099	13.6568
17	0.6606	-1.5788	-0.5414	2.1604	0.0263	0.1756	0.0514	-0.0592	0.0741	0.0107	0.0253	0.0643	0.0367	0.0063	-0.0767	0.0466	-0.0089	-0.0255	0.105	-0.0041	0.0772	12.6514	-2.7214	23.8987
18	8.922	9.2813	-7.228	14.7175	-9.7708	7.065	0.0215	-0.0186	0.1657	-0.2317	-0.0381	0.1306	0.1584	-0.0324	0.0166	0.0797	0.003	-0.028	0.109	0.0077	0.0824	9.1931	17.4387	15.9156
19	8.3574	14.1549	1.2016	18.8973	11.3019	11.5726	-0.0066	0.1034	0.8578	-1.0943	0.7364	0.7898	-1.0141	1.0632	-0.7298	0.2373	-0.0295	0.0069	0.1812	0.0583	0.1989	17.9688	25.7294	3.5425
20	5.4248	5.5407	-4.6839	8.2379	-5.3243	3.9476	0.1348	-0.1079	-0.0085	0.1466	-0.1324	0.2347	-0.1677	0.0526	-0.0024	0.0583	-0.0164	-0.0348	0.127	0.0188	0.0639	10.3589	14.6032	20.4343

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 11
2	X-RAY DIFFRACTION	2	A	12 - 26
3	X-RAY DIFFRACTION	3	A	27 - 34
4	X-RAY DIFFRACTION	4	A	35 - 41
5	X-RAY DIFFRACTION	5	A	42 - 53
6	X-RAY DIFFRACTION	6	A	54 - 71
7	X-RAY DIFFRACTION	7	A	72 - 84
8	X-RAY DIFFRACTION	8	A	85 - 96
9	X-RAY DIFFRACTION	9	A	97 - 105
10	X-RAY DIFFRACTION	10	A	106 - 114
11	X-RAY DIFFRACTION	11	A	115 - 128
12	X-RAY DIFFRACTION	12	A	129 - 140
13	X-RAY DIFFRACTION	13	A	141 - 146
14	X-RAY DIFFRACTION	14	A	147 - 160
15	X-RAY DIFFRACTION	15	A	161 - 177
16	X-RAY DIFFRACTION	16	A	178 - 182
17	X-RAY DIFFRACTION	17	A	183 - 195
18	X-RAY DIFFRACTION	18	A	196 - 202
19	X-RAY DIFFRACTION	19	A	203 - 209
20	X-RAY DIFFRACTION	20	A	210 - 222

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