PDB-6uam: Apo-form Dimer of Y77A Mutant Putative Ryanodine Receptor from Ba...

ID or keywords:

Entry

Database: PDB / ID: 6uam

Title

Apo-form Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482

Components

Putative ryanodine receptor

Keywords

METAL TRANSPORT / Alpha Fold / PSI-BIOLOGY / MCSG / Structural Genomics / Midwest Center for Structural Genomics

Function / homology

Ryanodine receptor Ryr / RyR domain / : / calcium ion transport / metal ion binding / CITRIC ACID / Ryanodine receptor

Function and homology information

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.802 Å

Authors

Wu, R. / Joachimiak, A. / Jedrzejczak, R. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Apo-form Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482
Authors: Wu, R. / Joachimiak, A. / Jedrzejczak, R.

History

Deposition	Sep 11, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uam.cif.gz	252.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6uam.ent.gz	207 KB	Display	PDB format
PDBx/mmJSON format	6uam.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6uam_validation.pdf.gz	488.9 KB	Display	wwPDB validaton report
Full document	6uam_full_validation.pdf.gz	501.1 KB	Display
Data in XML	6uam_validation.xml.gz	26.1 KB	Display
Data in CIF	6uam_validation.cif.gz	33.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ua/6uam ftp://data.pdbj.org/pub/pdb/validation_reports/ua/6uam	HTTPS FTP

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Related structure data

Similar structure data	2axa-d 5f8b-d 3nrt-1 6a6k-1 4rz2-2 3c37-1 5hcv-1 5c5g-d 2abi-2 2ax7-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative ryanodine receptor

B: Putative ryanodine receptor

C: Putative ryanodine receptor

D: Putative ryanodine receptor

E: Putative ryanodine receptor

F: Putative ryanodine receptor

hetero molecules

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

1

A: Putative ryanodine receptor

B: Putative ryanodine receptor

hetero molecules

defined by author&software
Evidence: gel filtration
24.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Putative ryanodine receptor

D: Putative ryanodine receptor

hetero molecules

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

3

E: Putative ryanodine receptor

F: Putative ryanodine receptor

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.623, 89.993, 74.482
Angle α, β, γ (deg.)	90.000, 110.890, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative ryanodine receptor Mass: 12001.018 Da / Num. of mol.: 6 / Mutation: Y77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2247 / Plasmid: pMCSG50 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8A5J2
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.3 Å³/Da / Density % sol: 62.69 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.5M sodium citrate, 0.1M Bis-tris

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97927 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2013

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97927 Å / Relative weight: 1

Reflection

Resolution: 2.8→50 Å / Num. obs: 22375 / % possible obs: 98.4 % / Redundancy: 3.2 % / R_merge(I) obs: 0.105 / Χ²: 0.792 / Net I/σ(I): 9.4 / Num. measured all: 72329

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.8-2.85	3.4	0.665	1135	0.907	1	99.7
2.85-2.9	3.4	0.62	1127	0.905	1	99.7
2.9-2.96	3.4	0.466	1114	0.929	1	99.9
2.96-3.02	3.3	0.362	1141	0.938	1	99.7
3.02-3.08	3.4	0.338	1142	0.921	1	99.7
3.08-3.15	3.3	0.301	1120	0.843	1	99.8
3.15-3.23	3.3	0.253	1126	0.904	1	99.6
3.23-3.32	3.3	0.199	1117	0.884	1	99.5
3.32-3.42	3.3	0.15	1132	0.838	1	99.2
3.42-3.53	3.3	0.119	1120	0.853	1	99
3.53-3.65	3.3	0.101	1116	0.843	1	99.4
3.65-3.8	3.3	0.084	1105	0.776	1	98.2
3.8-3.97	3.2	0.073	1120	0.751	1	98.4
3.97-4.18	3.2	0.062	1098	0.705	1	96.8
4.18-4.44	3.1	0.056	1107	0.644	1	96.9
4.44-4.79	3.1	0.047	1092	0.589	1	97.4
4.79-5.27	3.1	0.047	1145	0.55	1	97.4
5.27-6.03	3.1	0.053	1092	0.593	1	97.2
6.03-7.59	3.2	0.052	1129	0.627	1	96.7
7.59-50	2.8	0.052	1097	0.683	1	93.2

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.802→37.806 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.15

	R_factor	Num. reflection	% reflection
R_free	0.2531	1132	5.09 %
R_work	0.189	-	-
obs	0.1923	22240	97.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 159.92 Å² / B_iso mean: 52.3896 Å² / B_iso min: 15.75 Å²

Refinement step

Cycle: final / Resolution: 2.802→37.806 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4649	0	102	17	4768
B_iso mean	-	-	83	50.47	-
Num. residues	-	-	-	-	564

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.8022-2.9297	0.3403	133	0.2545	2615	97
2.9297-3.0841	0.3257	161	0.2345	2668	100
3.0841-3.2773	0.3066	138	0.221	2652	100
3.2773-3.5301	0.2813	145	0.1917	2692	99
3.5301-3.8851	0.2622	142	0.1786	2680	99
3.8851-4.4465	0.2123	129	0.1581	2662	99
4.4465-5.5992	0.2112	150	0.1678	2644	98
5.5992-37.806	0.221	134	0.1878	2495	91

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	3.1991	2.5107	-0.0565	2.8786	-0.1423	1.5064	-0.225	0.4827	0.1541	0.2724	0.4013	-0.1651	0.9661	1.1927	-0.1496	0.2378	-0.074	-0.0022	0.7658	-0.0918	0.327	29.4276	-5.3525	37.4618
2	4.6278	1.8562	0.7672	2.7601	1.4117	4.7814	0.0182	-0.0491	0.3838	0.135	0.2748	-0.0165	-0.4884	0.0598	-0.3276	0.2387	0.0581	-0.0478	0.3368	-0.0685	0.3205	14.0357	8.3941	45.489
3	6.5956	0.2862	0.1494	4.0071	-1.918	5.4715	-0.2805	0.5233	0.3935	-0.0872	-0.0349	-0.7582	-0.9071	0.3574	0.2374	0.7975	-0.0482	0.0226	0.4994	-0.0981	1.0289	22.8536	24.9853	41.5746
4	1.0936	-1.1729	0.2503	1.1347	-0.5514	2.7885	-0.1934	-0.297	2.3478	-0.2865	0.0624	-0.3895	-1.0972	0.3308	-0.0895	0.6819	-0.0622	0.0781	0.603	-0.1818	1.0175	21.1482	23.517	42.8285
5	4.0016	-3.0618	2.2779	2.6801	-3.282	4.9017	0.0045	-0.1079	0.3469	-0.6688	0.2414	-0.1739	-0.1349	-0.3255	-0.102	0.294	-0.0242	-0.0463	0.3026	-0.025	0.3399	17.7868	3.7784	38.6417
6	2.0716	-1.4505	1.9785	0.3195	-0.7686	2.7716	-0.0793	-0.7221	-0.7164	-0.1267	0.2919	-0.3512	1.0675	-0.9727	-0.2282	0.5292	-0.0677	-0.0707	0.3023	0.0017	0.5154	14.9556	-11.9895	48.7704
7	1.1369	0.4392	0.2103	0.1507	0.0608	-0.001	-0.3212	0.4518	1.2867	-0.2291	-0.1267	0.5018	-1.415	-0.4572	0.4358	1.3228	0.0119	-0.0699	1.3153	0.1858	1.0907	7.9016	26.5517	45.0847
8	3.1975	1.119	-2.0601	2.1386	0.7675	2.331	0.2759	-0.7698	0.4398	0.305	0.3487	0.3746	-0.2488	-0.8856	-0.4953	0.5977	0.186	-0.0522	0.6062	-0.1069	0.385	11.865	5.8528	55.7291
9	3.733	2.06	-3.3687	5.7185	-4.0158	8.8318	-0.1235	0.051	-0.0132	0.0333	-0.0999	-0.6054	-0.2738	0.2074	0.2593	0.2075	0.0324	-0.0274	0.3729	-0.0274	0.24	29.879	0.6896	44.2893
10	2.9448	-0.9136	1.385	3.5066	0.3218	1.0993	-0.2154	0.1513	1.0168	-1.0402	-0.0241	-0.523	-0.9055	0.3107	-0.0396	0.6859	-0.102	0.1272	0.616	0.2443	0.6483	36.7879	16.1356	38.1585
11	2.4561	3.4512	1.019	3.3792	0.4439	2.6189	0.4369	-0.9573	0.0632	0.4321	-0.4704	-0.2179	-0.0703	0.2885	0.0181	0.3008	-0.0037	-0.0792	0.4864	-0.0139	0.3043	25.624	4.1218	51.3383
12	1.9249	1.8164	5.493	1.9447	-4.8178	3.5705	0.8162	0.2734	-1.5078	0.7487	-1.0436	0.6381	1.2804	-0.9846	-0.0717	0.2197	-0.0279	-0.1697	0.7029	0.043	0.448	13.9858	-10.8487	51.1713
13	2.1395	0.1063	-2.0421	2.7419	-1.5972	2.9941	0.0375	-0.3285	-1.2236	0.0756	-0.0379	-0.6149	0.2136	0.0238	-0.0311	0.3293	0.0526	-0.0813	0.4748	-0.1086	0.303	-1.2777	-16.906	28.6464
14	2.4639	-4.4661	-2.5454	4.6191	1.0799	2.3238	0.1207	-0.692	0.7707	0.0072	0.016	-0.3874	-0.0479	-0.101	-0.0658	0.187	-0.009	-0.057	0.2426	0.0808	0.2614	-1.8752	4.6085	32.5931
15	9.0334	-1.913	0.8382	3.7626	-1.395	4.2134	0.3127	-0.3871	0.0778	0.2702	0.0541	0.0654	0.196	-0.3901	-0.3098	0.2845	0.0144	-0.033	0.4111	-0.0978	0.2994	-14.3876	5.4995	41.3685
16	3.4289	-0.964	-1.7358	5.1778	5.4318	2.4176	-0.271	-0.2736	-0.1727	0.3325	0.0236	0.6845	0.9364	0.3547	0.149	0.2554	0.0076	-0.0309	0.2354	0.0856	0.2983	0.6826	-5.9384	32.8478
17	2.1997	9.105	6.6704	2.237	6.3396	5.2751	0.1221	0.908	0.845	-1.641	-0.1194	-1.0056	-0.4222	1.2299	-0.1707	0.5349	0.1242	0.0526	0.7322	-0.1179	0.3392	11.4244	-2.975	19.2321
18	3.2341	-1.5591	-2.4503	3.3738	1.9457	3.7311	0.2395	-0.355	0.3535	-0.6131	0.0277	-0.0742	-1.019	0.0096	-0.266	0.2475	0.0247	-0.0754	0.5617	-0.0363	0.3229	-3.218	10.9422	25.7932
19	3.9166	1.7498	-4.1905	2.5898	-2.6277	6.7703	-0.2032	0.0032	-0.3119	-0.0983	-0.2454	0.0556	0.4047	-0.2441	0.3749	0.201	0.004	0.0007	0.3054	-0.0573	0.2587	-11.577	-10.8733	28.8143
20	5.2722	0.5552	-3.9174	1.9162	-2.0681	4.6508	-0.1297	0.3805	0.0679	-0.1058	0.0873	0.0444	0.0921	-0.4115	0.2222	0.2936	-0.0594	-0.0446	0.3144	0.0226	0.2326	-19.4308	-11.4793	32.1604
21	4.7198	1.8814	2.4472	4.3329	-0.1489	5.8378	-0.1095	0.4413	0.4132	0.0387	0.0966	-0.094	-0.1409	0.4607	0.0181	0.2889	0.0024	-0.0114	0.2665	0.0115	0.1652	-1.4585	-0.969	20.7855
22	4.4564	-1.5363	-0.3628	9.3946	-1.5905	4.9532	-0.2074	-0.8655	-0.897	1.122	0.3633	-0.1278	0.0314	-0.7277	-0.1016	0.4048	-0.1885	-0.1006	0.484	0.114	0.4191	-22.0851	-15.5723	4.9434
23	6.9327	-3.1551	-1.2709	6.0831	0.5025	2.8165	0.5254	-0.2282	-0.2975	-0.6814	-0.1822	-0.0259	0.0341	0.5013	-0.0069	0.1702	-0.0464	-0.0347	0.5378	-0.0347	0.266	-7.4435	-6.2317	-8.9623
24	5.8805	-2.7101	-1.7337	4.7975	2.2207	1.5082	0.0129	-0.0086	-1.1466	0.0873	-0.0728	0.0177	1.1645	0.9737	0.1253	0.6178	0.1667	0.0308	0.5847	-0.0338	0.6106	2.1857	-22.0494	-12.0011
25	5.5314	-1.6264	-4.1077	3.197	3.3267	2.8934	0.0476	0.6246	-0.5033	-0.0867	-0.279	0.3458	0.2554	-0.3422	0.2753	0.4197	0.0861	-0.0674	0.2769	-0.0595	0.2819	-14.5217	-10.1664	-7.7378
26	4.5416	-0.5908	0.7847	1.9787	1.8151	1.9622	-0.1109	-0.6817	0.7519	0.3277	-0.2568	0.5124	-1.3403	-0.4402	0.1546	0.6857	0.0497	0.093	0.4509	-0.116	0.3501	-18.8626	5.8844	2.7038
27	1.6546	-0.9793	-1.109	4.3093	3.4862	7.5706	-0.0443	0.6556	0.2234	-0.3249	-0.1861	-0.0282	-1.5932	0.5972	0.2071	0.4776	0.0729	0.0335	0.7297	-0.0213	0.2733	-0.3906	-0.708	-5.9934
28	2.643	1.0309	-0.115	10.1502	1.5992	4.1151	-0.0322	0.0715	-0.367	0.061	-0.097	0.478	0.5069	-0.1842	0.0631	0.2905	-0.0607	0.038	0.3704	0.0185	0.2651	-13.4043	-13.8194	6.0281
29	4.5947	-2.4101	-0.4693	2.016	1.9969	3.7643	0.437	1.1641	0.0147	-0.6064	-1.3046	-0.6369	2.0386	0.8976	0.0789	1.2928	-0.2335	0.3735	0.2413	-0.2401	1.1129	-8.0686	-31.6753	-3.0587
30	6.8453	0.4854	1.6512	6.4866	-1.1319	2.1007	0.2066	-0.2128	-0.9507	0.2325	0.0473	-0.341	-0.0564	-0.7187	-0.0609	0.4988	-0.0174	-0.039	0.449	0.14	0.5002	-7.7501	-23.3815	7.3108
31	4.7894	-1.9384	1.8139	8.5013	-3.366	3.6452	-0.1748	0.1084	0.0481	0.2362	-0.066	-0.3859	0.2647	0.3199	0.1913	0.2624	0.0311	-0.0381	0.2374	-0.0088	0.2091	-5.5135	-7.0576	2.9042
32	5.3806	0.5591	-2.6726	3.3846	0.2717	2.0257	-0.3384	-0.8723	0.767	0.3167	-0.0024	0.3571	-1.3968	-1.5254	0.3012	0.6558	0.2045	-0.1219	0.3901	-0.0896	0.4914	-17.0414	6.0635	4.8511

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 21 )	A	7 - 21
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 46 )	A	22 - 46
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 56 )	A	47 - 56
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 57 through 66 )	A	57 - 66
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 67 through 91 )	A	67 - 91
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 92 through 99 )	A	92 - 99
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 8 )	B	4 - 8
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 9 through 21 )	B	9 - 21
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 22 through 46 )	B	22 - 46
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 47 through 66 )	B	47 - 66
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 67 through 91 )	B	67 - 91
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 92 through 99 )	B	92 - 99
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 7 through 21 )	C	7 - 21
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 22 through 45 )	C	22 - 45
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 46 through 71 )	C	46 - 71
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 72 through 91 )	C	72 - 91
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 92 through 100 )	C	92 - 100
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 7 through 21 )	D	7 - 21
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 22 through 55 )	D	22 - 55
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 56 through 71 )	D	56 - 71
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 72 through 100 )	D	72 - 100
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 6 through 21 )	E	6 - 21
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 22 through 45 )	E	22 - 45
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 46 through 65 )	E	46 - 65
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 66 through 91 )	E	66 - 91
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 92 through 100 )	E	92 - 100
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 7 through 21 )	F	7 - 21
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 22 through 45 )	F	22 - 45
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 46 through 60 )	F	46 - 60
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 61 through 71 )	F	61 - 71
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 72 through 91 )	F	72 - 91
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 92 through 100 )	F	92 - 100

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