PDB-4n05: The crystal structure of R43A mutant putative ryanodine receptor ...

ID or keywords:

Entry

Database: PDB / ID: 4n05

Title

The crystal structure of R43A mutant putative ryanodine receptor from Bacteroides Thetaiotaomicron VPI-5482

Components

Putative ryanodine receptor

Keywords

UNKNOWN FUNCTION / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PUTATIVE RYANODINE RECEPTOR / ALPHA FOLD

Function / homology

Function and homology information

ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / calcium channel complex / sarcolemma / Z disc / metal ion binding
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.605 Å

Authors

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

Citation

Journal: TO BE PUBLISHED
Title: The crystal structure of R43A mutant putative ryanodine receptor from Bacteroides Thetaiotaomicron VPI-5482
Authors: Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Oct 1, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4n05.cif.gz	244.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4n05.ent.gz	210.3 KB	Display	PDB format
PDBx/mmJSON format	4n05.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4n05_validation.pdf.gz	477.5 KB	Display	wwPDB validaton report
Full document	4n05_full_validation.pdf.gz	484 KB	Display
Data in XML	4n05_validation.xml.gz	22.2 KB	Display
Data in CIF	4n05_validation.cif.gz	30.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n0/4n05 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n05	HTTPS FTP

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Related structure data

Similar structure data	6uhi-d 3nrt-1 6uag-3 2sgp-d 6uag-2 3fli-d 3mu7-d 1rz3-d 2fsq-d 6ug5-1 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
Other databases	TargetTrack: MCSG-APC106682

Similar structure data

Other databases

TargetTrack: MCSG-APC106682

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Putative ryanodine receptor

A: Putative ryanodine receptor

C: Putative ryanodine receptor

D: Putative ryanodine receptor

E: Putative ryanodine receptor

F: Putative ryanodine receptor

hetero molecules

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

1

B: Putative ryanodine receptor

A: Putative ryanodine receptor

hetero molecules

defined by author&software
24.8 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
24.7 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
24.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.362, 88.673, 74.370
Angle α, β, γ (deg.)	90.00, 111.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative ryanodine receptor Mass: 12279.257 Da / Num. of mol.: 6 / Mutation: R43A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_2247 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: Q8A5J2
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.15 Å³/Da / Density % sol: 61 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 1.5M NA CITRATE, 0.1M BISTRIS 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012 / Details: MIRRORS
Radiation	Monochromator: SI111, CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97904 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. all: 26789 / Num. obs: 26789 / % possible obs: 97.2 % / Redundancy: 3.7 % / R_sym value: 0.102 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4 / R_sym value: 0.454 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.605→42.12 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.25	1325	4.97 %
R_work	0.1843	-	-
obs	0.1875	26676	96.25 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.605→42.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4617	0	30	95	4742

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4753
X-RAY DIFFRACTION	f_angle_d	1.045	6418
X-RAY DIFFRACTION	f_dihedral_angle_d	16.156	1861
X-RAY DIFFRACTION	f_chiral_restr	0.072	681
X-RAY DIFFRACTION	f_plane_restr	0.005	834

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 (%)
2.6049-2.7092	0.2898	128	0.2206	2647	X-RAY DIFFRACTION	91
2.7092-2.8324	0.3331	163	0.2322	2808	X-RAY DIFFRACTION	98
2.8324-2.9817	0.2767	153	0.216	2885	X-RAY DIFFRACTION	98
2.9817-3.1685	0.2736	154	0.2042	2806	X-RAY DIFFRACTION	98
3.1685-3.413	0.2967	144	0.1822	2923	X-RAY DIFFRACTION	98
3.413-3.7563	0.2204	161	0.1755	2821	X-RAY DIFFRACTION	98
3.7563-4.2994	0.2485	140	0.1542	2853	X-RAY DIFFRACTION	97
4.2994-5.415	0.2227	149	0.1604	2793	X-RAY DIFFRACTION	95
5.415-42.1252	0.2268	133	0.2004	2815	X-RAY DIFFRACTION	93

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	0.0923	0.0299	0.0972	0.1814	0.0519	0.0398	0.1833	0.2883	-0.0307	-0.3924	-0.1989	0.2621	-0.6911	-0.135	-0.0001	0.4493	0.0013	-0.0091	0.4296	-0.0288	0.3929	-2.9017	13.831	25.9646
2	0.3761	0.1246	0.3167	0.1838	-0.0302	0.3212	0.0962	-0.0719	-0.077	0.0242	-0.1389	0.0326	-0.0132	0.0109	0.0001	0.4009	0.0026	0.0389	0.3652	0.0339	0.3007	-11.8086	-7.626	28.8402
3	0.1342	-0.0066	0.102	0.1705	-0.0577	0.0655	-0.1107	0.0588	-0.0001	0.057	0.1402	0.2119	-0.1397	-0.4584	-0	0.426	-0.0887	0.0255	0.4887	-0.0148	0.3655	-19.344	-8.6976	31.4055
4	0.1194	0.0222	-0.0913	0.1312	-0.2143	0.3336	0.1316	0.498	0.5916	0.3301	-0.1916	0.0977	-0.0624	-0.6033	-0.0013	0.3798	0.0263	-0.0244	0.2593	0.0234	0.3242	-5.9612	3.3532	22.8827
5	0.004	-0.0443	0.0047	0.0485	0.0273	0.035	-0.1753	0.2391	0.0361	0.4432	-0.0118	-0.0022	-0.089	-0.0767	-0.0003	0.3972	-0.0184	-0.0203	0.5233	0.0266	0.4306	10.1821	0.2633	17.0646
6	-0.0043	0.066	0.024	0.1527	-0.0441	-0.0253	0.1104	-0.1634	-0.5964	-0.0147	-0.1385	-0.1857	0.1248	0.1417	0	0.4205	-0.0117	0.0026	0.5264	-0.0095	0.4147	-1.4389	-13.9229	28.1207
7	0.0625	-0.0643	0.1535	0.2493	0.0837	0.4557	0.2234	-0.0955	0.0614	-0.0986	-0.2039	-0.008	-0.1454	-0.0073	0	0.2459	0.0395	-0.0039	0.2652	-0.0242	0.3801	-4.8048	8.0648	33.7705
8	0.0453	-0.0562	-0.0042	0.1186	0.0482	-0.0001	0.1756	-0.3958	-0.0261	0.5814	0.257	0.0154	0.2105	-0.4975	0.0001	0.3803	-0.0219	0.0245	0.5719	-0.0405	0.454	-18.5265	7.4946	41.8757
9	0.2418	-0.2135	0.0912	0.14	-0.2502	0.2836	-0.0661	-0.1824	0.0347	0.0098	0.0184	0.1747	0.2081	0.0107	0	0.3129	-0.0008	-0.0512	0.3592	-0.0033	0.3583	-0.442	-0.9485	34.6981
10	0.034	-0.0695	0.0201	0.2341	-0.0805	0.036	0.1236	0.1138	0.1409	-0.5188	-0.6652	-0.2624	0.281	0.8835	-0.0181	0.3832	-0.0002	0.0453	0.6354	0.1027	0.5164	11.571	-0.2106	19.1366
11	0.0448	-0.1428	0.2093	-0.1673	-0.0677	0.8886	0.0298	0.0411	-0.0256	0.0175	0.1701	-0.0828	0.3082	-0.0568	-0.0001	0.4266	-0.0556	0.0161	0.3951	0.0118	0.2581	-8.9432	-5.4433	1.3964
12	0.1199	-0.1981	-0.0226	0.1393	0.0848	0.0944	-0.1386	0.0072	-0.6042	-0.4544	0.5511	-0.0455	0.2171	0.2238	0.2162	1.3781	-0.3171	0.592	0.2032	-0.6897	0.7456	-9.0292	-26.794	-1.1162
13	0.3954	0.2717	0.2723	0.1587	0.2158	0.231	-0.0498	0.027	-0.0588	0.2616	0.0032	0.01	0.0461	0.3788	0.0001	0.4516	0.0001	0.0507	0.4363	-0.0121	0.3193	-6.0416	-6.6324	3.8975
14	0.7086	0.0102	0.6846	0.0031	0.0041	0.6751	-0.1325	-0.6853	0.5879	0.0616	0.0053	-0.1706	-0.4634	-0.3068	-0.0154	0.5261	0.0173	-0.02	0.2932	-0.0592	0.257	-16.7724	9.6373	4.6152
15	0.1016	-0.056	-0.1822	0.0478	0.1113	0.2075	0.0228	0.1387	-0.363	-0.6771	0.4229	0.3777	0.4486	-0.6848	0	0.554	-0.0118	-0.053	0.5465	0.0174	0.5117	-23.1279	-9.8808	4.6309
16	0.289	0.3803	-0.0625	0.7481	0.0358	0.3307	0.1105	-0.1962	-0.1114	-0.5881	-0.2361	0.0129	0.1143	0.2624	-0.0215	0.3608	0.0643	0.0816	0.5864	0.0436	0.337	-4.2061	-6.9222	-9.1758
17	-0.0033	0.0026	0.0183	0.0563	0.0522	0.031	0.1021	0.1755	0.0445	0.0508	0.4193	0.2196	-0.0063	0.2663	-0	0.5566	0.2401	0.1835	0.5974	-0.0138	0.7407	2.7478	-16.3957	-10.3778
18	0.3074	0.2102	0.1453	0.1378	0.1619	0.0773	0.1536	0.1629	-0.2377	-0.1275	-0.069	0.0887	-0.1009	-0.1059	0.0002	0.3715	0.0145	-0.0062	0.2829	0.0158	0.3037	-14.7085	-6.9736	-6.227
19	2.7763	-0.3873	0.578	1.4623	-1.3383	1.2088	-0.2965	-0.4946	0.5608	0.2865	0.284	0.6391	-1.2253	-0.2373	-0.2021	0.6153	0.1018	-0.1497	0.2668	-0.0833	0.406	-19.0976	10.3225	1.7773
20	0.201	-0.1243	0.0966	0.0241	-0.1778	0.0912	0.0982	0.4629	-0.3167	-0.0142	0.104	-0.0509	0.1226	0.2964	0.0084	0.2726	-0.0581	0.0092	0.6212	0.01	0.5101	29.4346	-2.8067	37.2872
21	0.7477	-0.2258	0.1568	0.3154	0.1159	1.5329	0.0098	-0.25	0.3998	0.2166	0.7347	-0.6956	-0.0042	-0.1762	0.3351	0.2233	0.0933	0.0677	0.2888	-0.2169	0.5735	14.2715	13.1928	45.8463
22	0.0036	-0.004	-0.0059	0.0032	0.0029	0.0116	-0.2189	0.0973	-0.498	-0.2622	-0.2463	-0.2352	-0.1127	-0.1052	-0.0007	1.1777	-0.1216	0.1744	0.8309	-0.1896	2.1566	25.1058	27.4769	40.2185
23	0.2922	0.122	-0.0337	0.0639	-0.0666	0.0249	0.0984	0.1278	0.0742	-0.0048	0.5146	-0.224	-0.1508	0.1409	0.1456	0.4737	-0.2137	0.3324	0.0575	-0.5484	1.9277	20.8432	25.7441	44.3727
24	0.3422	0.1086	-0.3392	0.2764	0.1895	0.54	0.0725	0.1569	0.3505	-0.3806	-0.0589	-0.0908	0.214	-0.0474	-0.0001	0.3225	0.0246	-0.0436	0.4995	0.0157	0.463	18.0495	6.5249	38.9114
25	0.0627	0.0889	0.2292	0.1254	0.2962	0.7514	-0.0591	-0.0664	-0.5511	0.323	0.0567	-0.0017	1.0229	-0.5747	0.0184	0.4562	-0.1024	-0.0325	0.4207	0.0931	0.5159	13.4421	-9.6641	48.9133
26	0.0413	-0.0406	-0.0694	0.0202	0.0305	0.0272	0.0069	-0.6605	0.7216	-0.0208	0.4161	0.2628	-0.0417	0.2688	-0.0004	0.6504	0.0661	-0.0704	0.469	-0.0366	0.5873	9.5407	13.6256	53.3918
27	0.0155	0.0382	0.0015	0.1149	-0.042	0.0405	-0.1681	-0.4733	-0.3068	0.2774	0.2012	0.1338	0.0419	-0.6808	-0	0.3743	-0.0395	-0.0753	0.5331	-0.0151	0.2794	21.6051	-2.8675	57.481
28	0.0643	0.0111	-0.0293	0.0191	0.0175	0.0079	0.4056	0.1565	-0.4392	0.1127	-0.287	-0.22	-0.0572	0.5443	-0.0004	0.2912	-0.0023	0.0018	0.6037	0.0245	0.3632	30.5212	1.7444	46.0791
29	0.1876	0.1688	-0.4231	0.1361	-0.3681	1.0549	-0.2092	0.3537	-0.0121	-0.5212	-0.0752	-0.4311	0.1137	0.1159	-0.2508	0.3454	0.0695	0.3902	1.4338	0.7714	0.1705	31.6898	8.6107	32.5887
30	0.0023	0.0131	-0.0136	0.0035	0.0083	0.0034	-0.6929	-0.0831	0.7413	-0.067	0.2171	-0.3506	0.3119	-0.0033	0.0002	0.8046	-0.1524	0.0999	0.9635	0.0983	1.2081	34.9374	20.5332	34.6696
31	0.1346	0.0948	0.0847	0.0561	0.0584	0.0816	-0.0772	-0.0014	-0.0931	-0.0819	-0.0019	0.1142	-0.0973	0.0072	-0.0053	0.8644	0.0846	0.6482	0.5191	1.014	0.929	34.4083	15.7867	38.2527
32	-0.0007	-0.0098	-0.0162	0.0135	0.008	0.0417	0.2713	0.3153	0.5739	0.2896	-0.006	-0.228	-0.049	0.6753	0.0003	0.498	-0.0928	0.0381	0.6958	0.0377	0.5703	35.7913	10.3934	48.3305
33	0.045	0.0081	0.0224	0.0861	0.0873	0.0458	0.653	-0.082	-0.2023	0.2653	-0.1004	0.3857	-0.534	0.2806	-0.0003	0.3783	0.0271	0.0122	0.4019	0.0307	0.3737	24.9939	7.7656	51.586
34	0.4388	-0.0135	0.0898	0.0378	-0.1371	0.6531	-0.1517	-0.0301	0.2795	-0.1194	0.3924	-0.1391	-0.3005	0.274	0.0392	0.29	0.0023	0.0139	0.169	-0.0514	0.3305	14.2797	2.6299	50.2192
35	0.0097	-0.0016	-0.0143	0.0102	-0.0174	0.017	0.1051	-0.1321	-0.2452	0.0304	0.3538	-0.1724	-0.0211	-0.3112	-0.0006	0.3103	-0.045	0.0257	0.6566	-0.1032	0.5063	8.8567	-1.3595	50.659
36	0.0222	0.0025	-0.002	0.0389	0.0129	0.0126	0.0649	-0.0385	-0.2242	-0.2228	-0.3755	-0.2933	0.2732	0.0269	0.0006	0.6271	-0.0629	-0.282	0.3792	-0.0059	0.6897	17.3714	-12.2569	52.5707

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 7 through 21 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 22 through 56 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 57 through 71 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 72 through 92 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 93 through 99 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 7 through 21 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 22 through 51 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 52 through 66 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 67 through 91 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 92 through 100 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 7 through 46 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 47 through 66 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 67 through 91 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 92 through 100 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 8 through 21 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 22 through 56 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 57 through 66 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 67 through 92 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 93 through 100 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 7 through 21 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 22 through 51 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 52 through 56 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 57 through 66 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 67 through 91 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 92 through 100 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 8 through 17 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 18 through 27 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 28 through 37 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 38 through 48 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 49 through 59 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 60 through 64 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 65 through 74 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 75 through 84 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 85 through 89 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 90 through 94 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 95 through 100 )

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