PDB-4jdx: Structure of the Fluorescence Recovery Protein from Synechocystis...

ID or keywords:

Entry

Database: PDB / ID: 4jdx

Title

Structure of the Fluorescence Recovery Protein from Synechocystis sp PCC 6803

Components

Slr1964 protein

Keywords

PROTEIN BINDING / photoprotection / non-photochemical quenching

Function / homology

Helix Hairpins - #1840 / Fluorescence recovery protein / : / Photoprotection regulator fluorescence recovery protein / Helix Hairpins / plasma membrane-derived thylakoid membrane / Helix non-globular / Special / Fluorescence recovery protein

Function and homology information

Biological species

Synechocystis sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Sutter, M. / Kerfeld, C.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of the FRP and identification of the active site for modulation of OCP-mediated photoprotection in cyanobacteria.
Authors: Sutter, M. / Wilson, A. / Leverenz, R.L. / Lopez-Igual, R. / Thurotte, A. / Salmeen, A.E. / Kirilovsky, D. / Kerfeld, C.A.

History

Deposition	Feb 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jun 12, 2013	Group: Database references
Revision 1.2	Jun 26, 2013	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jdx.cif.gz	348.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4jdx.ent.gz	296.9 KB	Display	PDB format
PDBx/mmJSON format	4jdx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4jdx_validation.pdf.gz	465.2 KB	Display	wwPDB validaton report
Full document	4jdx_full_validation.pdf.gz	470.5 KB	Display
Data in XML	4jdx_validation.xml.gz	21.1 KB	Display
Data in CIF	4jdx_validation.cif.gz	29.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jd/4jdx ftp://data.pdbj.org/pub/pdb/validation_reports/jd/4jdx	HTTPS FTP

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Related structure data

Related structure data	4jdqC C: citing same article (ref.)
Similar structure data	4jdq-1 4jdq-2 5tz0-d 1708 4fvj-4 6m97-d 3hls-6 6m98-d 1d4r-1 4fvj-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

4jdqC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Slr1964 protein

B: Slr1964 protein

C: Slr1964 protein

D: Slr1964 protein

E: Slr1964 protein

F: Slr1964 protein

79.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Slr1964 protein

C: Slr1964 protein

defined by author&software
26.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Slr1964 protein

D: Slr1964 protein

defined by author&software
26.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Slr1964 protein

F: Slr1964 protein

E: Slr1964 protein

F: Slr1964 protein

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

Unit cell

Length a, b, c (Å)	87.342, 87.342, 230.779
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	E-206- HOH

#1: Protein	Slr1964 protein Mass: 13214.956 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr1964 / Production host: Escherichia coli (E. coli) / References: UniProt: P74103
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.68 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 10% PEG-3350, 100mM Na-citrate, 2% tacsimate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976484 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2012
Radiation	Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976484 Å / Relative weight: 1
Reflection	Resolution: 2.5→39.061 Å / Num. obs: 31732 / % possible obs: 99.8 % / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.01191 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.5→39.05 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 27.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2637	2000	6.33 %	random
R_work	0.2162	-	-	-
obs	0.2192	31595	99.57 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→39.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4681	0	0	78	4759

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	4754
X-RAY DIFFRACTION	f_angle_d	0.469	6405
X-RAY DIFFRACTION	f_dihedral_angle_d	13.25	1745
X-RAY DIFFRACTION	f_chiral_restr	0.036	732
X-RAY DIFFRACTION	f_plane_restr	0.001	815

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 (%)
2.5-2.5656	0.3193	138	0.2953	2044	X-RAY DIFFRACTION	98
2.5656-2.6349	0.3737	139	0.2971	2055	X-RAY DIFFRACTION	99
2.6349-2.7124	0.3577	140	0.2854	2076	X-RAY DIFFRACTION	100
2.7124-2.8	0.3412	140	0.2767	2070	X-RAY DIFFRACTION	99
2.8-2.9	0.3405	140	0.2616	2064	X-RAY DIFFRACTION	100
2.9-3.0161	0.3188	142	0.2652	2101	X-RAY DIFFRACTION	100
3.0161-3.1533	0.2836	140	0.249	2086	X-RAY DIFFRACTION	100
3.1533-3.3195	0.3132	142	0.2417	2092	X-RAY DIFFRACTION	100
3.3195-3.5273	0.2569	143	0.2218	2116	X-RAY DIFFRACTION	100
3.5273-3.7994	0.2378	143	0.2008	2118	X-RAY DIFFRACTION	100
3.7994-4.1814	0.2546	144	0.1933	2121	X-RAY DIFFRACTION	100
4.1814-4.7855	0.2308	145	0.1827	2145	X-RAY DIFFRACTION	100
4.7855-6.0257	0.2575	147	0.2116	2184	X-RAY DIFFRACTION	100
6.0257-39.0653	0.2246	157	0.1934	2323	X-RAY DIFFRACTION	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	6.7469	-0.9097	2.6551	2.1285	-1.2775	3.1747	-0.4276	-0.2589	0.7048	0.2392	0.1721	-0.1841	-0.3593	-0.2978	0.1041	0.3051	-0.0224	0.0009	0.4817	-0.096	0.4224	85.394	-21.6246	81.296
2	5.1515	-2.0267	1.6976	2.3818	-0.5332	3.804	0.4696	0.6011	-0.9074	-0.4857	-0.1989	0.2693	0.6491	0.2515	-0.0801	0.4525	0.0153	-0.0137	0.6169	-0.1227	0.6579	101.0983	-34.0909	81.7564
3	4.7753	2.6584	-1.0648	2.9275	0.6686	5.0043	-0.1281	0.6563	-0.249	0.0763	0.072	-0.2672	0.0087	0.2639	-0.025	0.3469	0.0299	-0.0245	0.6519	-0.0843	0.4253	80.9432	-25.5389	71.3655
4	3.4355	-0.7728	0.4431	4.0245	1.7143	3.1431	0.3417	-0.1843	-0.25	0.2104	-0.1924	0.4041	0.7666	-0.4051	-0.0058	0.3917	-0.0538	-0.0381	0.5591	0.0069	0.4023	72.6226	-27.2969	77.1192
5	2.7114	-1.2631	0.1766	6.516	0.9291	3.3062	0.0428	0.5606	-0.7005	-0.0715	-0.0222	2.5662	0.1447	-0.3779	-0.141	0.6434	-0.0589	-0.0482	0.6923	0.1489	1.0952	73.9132	2.3513	33.4844
6	3.4519	1.5998	0.5446	7.0185	-3.0493	7.1208	-0.0594	-0.1091	-0.7357	0.6863	0.0706	-1.6305	-0.0482	1.4018	0.0704	0.889	0.0605	0.0847	0.76	0.0211	0.9535	85.0643	-12.4519	46.1689
7	6.3906	-0.3974	-0.4148	4.1354	2.5698	4.0511	-0.8379	-0.4929	0.5038	0.9059	0.0157	1.4022	0.4899	-0.1493	0.5797	0.618	0.0588	0.1807	0.7033	0.028	0.9052	76.7812	10.7437	39.9067
8	3.5004	-1.2937	-0.9003	5.7654	0.9198	2.7997	0.0821	-0.014	0.8757	-1.1074	0.4977	0.2958	-0.5971	-0.0337	-0.5555	0.6474	-0.0309	-0.0294	0.531	0.0985	0.7853	80.0056	16.4893	31.127
9	5.3994	2.4256	1.7494	2.0844	0.5131	2.2982	-0.3583	0.2071	1.0876	-0.2712	0.0817	0.3243	-0.1968	0.0379	0.1877	0.4123	0.0307	-0.0055	0.5406	-0.0491	0.5575	79.4038	-4.6009	86.0441
10	5.7058	0.8322	2.7806	-0.1181	0.1726	0.8168	-0.2458	-0.4511	-0.5656	-0.0796	0.2024	-0.3045	-0.3209	-0.1963	0.072	0.4134	-0.0387	-0.0081	0.7358	-0.0727	0.4468	69.3806	-13.789	92.2276
11	2.597	-0.2122	0.698	3.8362	-0.5556	4.3995	-0.0383	0.6112	-0.1643	-0.0426	-0.0526	-0.5623	0.0679	0.8856	0.0565	0.3945	0.0123	0.0416	0.618	-0.004	0.4735	91.6051	-10.2041	89.5324
12	3.8477	1.6301	-1.2062	3.6607	-0.6083	1.9866	-0.795	0.591	-0.9052	-0.6217	0.6579	0.0118	1.1031	0.9618	0.2204	1.383	0.1346	0.1153	1.0462	-0.2405	0.9251	84.5001	-31.0987	50.0712
13	2.5456	-0.3959	-0.3523	3.4032	-0.2818	5.5047	0.0732	0.0406	0.4224	-0.1574	0.3321	0.7337	0.5968	-0.037	-0.3245	0.7799	-0.1226	-0.1661	0.7716	0.136	1.0374	75.328	-14.2922	47.8084
14	5.9686	0.1446	0.9923	6.3743	-1.8549	8.6179	-0.866	-1.1672	0.3006	-1.0115	-0.9689	-0.9234	0.2489	0.1736	1.5063	0.6584	0.0403	0.1281	1.1535	-0.1078	0.8596	87.4891	-28.8421	63.7536
15	1.8724	0.4177	-3.8469	6.2988	-0.3384	9.1864	-1.7624	-0.8176	0.2623	0.1637	0.2006	-0.2643	2.4225	0.4285	1.0446	1.2175	0.3153	-0.0205	0.9101	-0.1664	0.9383	79.2822	-34.8001	62.3411
16	1.7153	-1.4742	-2.553	3.9283	-1.3962	8.1236	-1.853	0.3461	-0.9662	-1.6509	0.4669	0.0698	3.8934	-0.703	0.9471	1.7528	-0.0304	0.2735	0.7084	-0.1258	1.3209	79.2935	-43.5334	61.8785
17	2.259	-1.8422	1.3617	3.0403	-1.6205	1.4439	0.0583	0.0275	-0.4623	-0.3644	-0.0705	0.1228	0.3839	0.2422	-0.094	0.7058	0.0627	0.1193	0.5272	-0.0291	0.5863	53.3651	24.4508	53.4235
18	6.716	1.0405	1.9384	2.2581	-0.5206	7.4203	0.262	-0.2159	-0.3421	-0.3795	0.1068	0.5883	0.0675	-0.9029	-0.3124	0.5443	-0.0393	-0.0282	0.5287	-0.0031	0.4947	27.3474	36.7065	49.0026
19	7.1803	-2.2012	1.6807	3.0236	-1.6144	2.1576	-0.0149	-0.1911	0.6273	-0.0199	-0.2111	-0.6578	0.1378	-0.0075	0.164	0.5577	0.0186	0.0757	0.4838	0.0239	0.4137	45.3303	32.2684	61.3719
20	3.7585	-0.7453	2.0571	4.7238	-1.7889	5.3446	0.6456	-0.035	0.2041	-0.1798	-0.2461	0.6029	1.2129	-0.5666	-0.2548	0.89	0.1258	-0.1285	0.7419	0.0679	0.8814	63.7586	2.9622	66.6436

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 8:41)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 42:66)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 67:83)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 84:109)
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESSEQ 8:41)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 42:63)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 64:84)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 85:109)
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESSEQ 8:42)
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESSEQ 43:73)
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESSEQ 74:109)
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESSEQ 12:42)
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESSEQ 43:63)
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESSEQ 64:72)
15	X-RAY DIFFRACTION	15	CHAIN D AND (RESSEQ 73:84)
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESSEQ 85:108)
17	X-RAY DIFFRACTION	17	CHAIN E AND (RESSEQ 12:57)
18	X-RAY DIFFRACTION	18	CHAIN E AND (RESSEQ 58:109)
19	X-RAY DIFFRACTION	19	CHAIN F AND (RESSEQ 8:53)
20	X-RAY DIFFRACTION	20	CHAIN F AND (RESSEQ 54:109)

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