PDB-5t1y: MLA10 coiled-coil fragment

ID or keywords:

Entry

Database: PDB / ID: 5t1y

Title

MLA10 coiled-coil fragment

Components

MLA10

Keywords

PLANT PROTEIN / coiled-coil

Function / homology

Function and homology information

response to other organism / ADP binding / defense response
Similarity search - Function

Biological species

Hordeum vulgare (barley)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.05 Å

Authors

Williams, S.J. / Kobe, B. / Bentham, A. / Ericsson, D.J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins.
Authors: Casey, L.W. / Lavrencic, P. / Bentham, A.R. / Cesari, S. / Ericsson, D.J. / Croll, T. / Turk, D. / Anderson, P.A. / Mark, A.E. / Dodds, P.N. / Mobli, M. / Kobe, B. / Williams, S.J.

History

Deposition	Aug 22, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 2, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t1y.cif.gz	370.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5t1y.ent.gz	319.7 KB	Display	PDB format
PDBx/mmJSON format	5t1y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5t1y_validation.pdf.gz	495.4 KB	Display	wwPDB validaton report
Full document	5t1y_full_validation.pdf.gz	505.8 KB	Display
Data in XML	5t1y_validation.xml.gz	33.1 KB	Display
Data in CIF	5t1y_validation.cif.gz	46 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t1/5t1y ftp://data.pdbj.org/pub/pdb/validation_reports/t1/5t1y	HTTPS FTP

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Related structure data

Related structure data	2ncgC C: citing same article (ref.)
Similar structure data	5b3d-2 4yv4-2 5uhq-2 4yv4-3 3aei-d 4ld3-d 1qc0-d 5uhq-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) 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) 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) 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

2ncgC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#177 - Sep 2014 Apoptosomes similarity (3)

Deposited unit

A: MLA10

B: MLA10

C: MLA10

D: MLA10

E: MLA10

F: MLA10

G: MLA10

H: MLA10

hetero molecules

108 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: MLA10

hetero molecules

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

2

B: MLA10

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

3

C: MLA10

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

4

D: MLA10

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

5

E: MLA10

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

6

F: MLA10

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

7

G: MLA10

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

8

H: MLA10

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

9

A: MLA10

B: MLA10

hetero molecules

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

10

C: MLA10

D: MLA10

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

11

E: MLA10

F: MLA10

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

12

G: MLA10

H: MLA10

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

Unit cell

Length a, b, c (Å)	30.720, 87.140, 92.247
Angle α, β, γ (deg.)	89.930, 90.000, 89.980
Int Tables number	1
Space group name H-M	P1

#1: Protein	MLA10 Mass: 13427.165 Da / Num. of mol.: 8 / Fragment: Coiled-coil domain (UNP residues 5-120) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Gene: Mla10 / Production host: Hordeum vulgare (barley) / References: UniProt: Q8GSK4
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.3 Å³/Da / Density % sol: 46.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Pact Premier, condition B4 (MIB buffer pH 7.0, 25% PEG 1500)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2015
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.05→46.12 Å / Num. obs: 58095 / % possible obs: 96.5 % / Redundancy: 1.8 % / B_iso Wilson estimate: 38.88 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.047 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.05→2.1 Å / R_merge(I) obs: 0.037

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Processing

Software

Name	Version	Classification
PHENIX	dev_2376	refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
Aimless		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.05→40.785 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.11

	R_factor	Num. reflection	% reflection
R_free	0.2788	5895	10.17 %
R_work	0.2515	-	-
obs	0.2543	57984	96.34 %

Solvent computation

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

Displacement parameters

B_iso max: 150.01 Å² / B_iso mean: 62.1511 Å² / B_iso min: 21.55 Å²

Refinement step

Cycle: final / Resolution: 2.05→40.785 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7147	0	10	215	7372
B_iso mean	-	-	69.79	51.48	-
Num. residues	-	-	-	-	903

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	7223
X-RAY DIFFRACTION	f_angle_d	0.348	9661
X-RAY DIFFRACTION	f_chiral_restr	0.03	1126
X-RAY DIFFRACTION	f_plane_restr	0.002	1222
X-RAY DIFFRACTION	f_dihedral_angle_d	10.636	4510

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0474-2.0707	0.4066	151	0.3767	1594	1745	88
2.0707-2.0951	0.3949	213	0.347	1654	1867	96
2.0951-2.1206	0.3275	201	0.3257	1683	1884	95
2.1206-2.1474	0.3544	223	0.3126	1783	2006	96
2.1474-2.1757	0.395	175	0.3244	1803	1978	97
2.1757-2.2055	0.3077	219	0.2781	1671	1890	97
2.2055-2.237	0.3311	191	0.2956	1699	1890	96
2.237-2.2704	0.342	185	0.2938	1739	1924	96
2.2704-2.3059	0.2751	194	0.2921	1765	1959	97
2.3059-2.3437	0.2988	227	0.2803	1760	1987	96
2.3437-2.3841	0.3336	188	0.2726	1680	1868	96
2.3841-2.4274	0.2511	187	0.257	1814	2001	97
2.4274-2.4741	0.3338	197	0.256	1673	1870	97
2.4741-2.5246	0.3147	248	0.258	1736	1984	97
2.5246-2.5795	0.2744	178	0.2736	1795	1973	97
2.5795-2.6395	0.3123	178	0.2637	1749	1927	97
2.6395-2.7055	0.3004	199	0.2551	1738	1937	97
2.7055-2.7786	0.2844	188	0.2655	1809	1997	97
2.7786-2.8604	0.2768	180	0.2617	1718	1898	97
2.8604-2.9526	0.3428	193	0.2768	1764	1957	97
2.9526-3.0581	0.2893	205	0.2741	1789	1994	97
3.0581-3.1805	0.3145	141	0.2604	1776	1917	97
3.1805-3.3252	0.3499	173	0.2696	1800	1973	97
3.3252-3.5005	0.2781	202	0.2437	1746	1948	97
3.5005-3.7196	0.2308	216	0.2303	1703	1919	97
3.7196-4.0066	0.2374	315	0.2228	1662	1977	97
4.0066-4.4094	0.2453	202	0.2377	1782	1984	97
4.4094-5.0464	0.2713	177	0.2078	1766	1943	97
5.0464-6.3541	0.2904	172	0.2736	1715	1887	96
6.3541-40.793	0.2272	177	0.206	1723	1900	94

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	1.1951	-0.5145	0.0035	0.2186	0.3098	1.6471	0.2715	0.2691	0.1678	-1.8319	-0.2071	-0.6863	-0.4112	0.0261	-0.0337	0.9175	0.0354	0.1211	0.4545	0.0911	0.3571	-40.7055	90.8874	-105.0904
2	4.5442	-1.6397	-0.8711	3.9193	1.3665	3.8536	-0.2358	0.0611	-0.6182	-0.0282	-0.045	0.837	0.6391	0.1251	-0.0328	0.47	0.0255	0.0498	0.2267	0.0294	0.1567	-41.7786	71.713	-97.5475
3	1.1757	-0.3163	0.2086	3.4755	-1.9278	3.6533	0.0064	0.4221	0.6437	-0.7239	0.4499	1.3765	0.0903	-1.2864	0.1199	0.9271	-0.0203	-0.1408	0.9739	0.3188	1.2454	-57.3437	111.8771	-97.4863
4	2.0221	-1.8649	-0.2822	1.8572	0.2394	2.6304	0.409	0.1643	0.2271	-1.5725	-0.7161	0.6066	-0.5823	-0.2517	0.1	0.7766	0.0947	-0.238	0.4867	-0.0171	0.4737	-49.5693	99.2456	-103.9406
5	1.4197	0.5602	0.4036	3.7521	-0.9539	3.51	-0.5113	-0.3603	0.7409	0.788	0.6677	0.3737	-0.9779	-0.544	0.0655	0.8402	0.1186	0.0258	0.4567	0.07	0.599	-49.8397	118.4823	-94.0743
6	3.4564	-1.4151	0.7234	0.6169	-0.9176	5.5892	0.4031	0.1126	0.4335	-0.9826	0.1512	-1.6536	-0.6145	0.0607	0.0488	0.7128	0.0357	0.1799	0.3932	0.0155	0.4343	-32.7256	73.0851	-104.404
7	1.4661	-1.5089	-0.0695	1.257	-0.3096	1.5692	0.305	0.2178	-0.2447	-1.722	-0.1129	0.4745	0.3899	-0.0254	-0.2481	0.8412	0.0065	-0.0843	0.4179	-0.0618	0.3642	-62.1177	127.3391	-150.9728
8	6.824	-0.9898	1.3104	2.4967	-0.7788	4.9423	-0.2143	0.0215	1.2892	-0.581	0.0344	-1.2385	-1.1261	-0.3726	0.1143	0.5825	0.0629	0.0842	0.1498	0.0015	-0.0858	-60.9389	149.4612	-144.7394
9	1.225	-0.5406	0.0353	5.0501	-0.6269	1.2306	0.0823	0.2861	-0.2936	-1.9373	0.3002	-1.0946	0.4969	1.0577	-0.2136	1.302	0.0477	0.1199	0.8575	-0.1604	1.129	-45.3444	107.1092	-143.5972
10	1.8172	-1.2131	0.3857	0.6562	-0.1016	1.6629	0.1538	0.1866	-0.1396	-1.4524	-0.3134	-0.518	0.4841	0.1928	-0.0223	0.9484	0.1036	0.3222	0.475	0.065	0.4692	-53.1507	119.8584	-150.0908
11	1.2517	0.4909	-0.902	5.8349	3.0027	3.2598	-0.3458	-0.1991	-0.5523	0.2682	0.4854	-0.8178	0.9876	0.5773	-0.1979	0.9081	0.1482	0.084	0.5132	0.0419	0.6537	-52.6025	99.9777	-140.2321
12	1.9137	-1.0146	-0.3881	2.2433	-1.6963	3.9813	0.1275	0.3445	-0.2751	-1.5267	0.5325	1.3577	0.5299	-0.2865	-0.1561	0.6659	0.0466	-0.125	0.3423	0.0062	0.4302	-69.7874	145.3709	-150.1223
13	1.6494	1.4953	0.4262	3.082	1.4391	2.8597	0.1327	-0.1524	-0.0123	1.1739	-0.1568	-0.0556	-0.1098	0.1429	-0.1307	0.5082	-0.0401	0.0169	0.3374	0.064	0.2243	-41.3323	92.5244	-77.503
14	0.6828	0.7092	0.8502	4.4625	-0.4779	1.8352	0.1286	-0.4536	-0.3709	1.519	0.0312	0.6877	-0.1466	-1.4112	0.0882	1.2277	-0.0452	0.1095	0.9091	0.1304	1.1598	-57.7004	61.8095	-81.21
15	1.2819	1.4807	0.0422	1.2093	0.2124	1.5119	0.252	-0.1503	-0.083	1.3565	-0.5314	1.3824	0.3649	-0.2795	-0.2275	0.8734	-0.1186	0.2595	0.4744	-0.0116	0.4765	-49.5439	76.4154	-75.1757
16	3.1782	-0.3074	0.4677	1.8078	-0.0911	2.4722	-0.1988	0.2184	-0.4812	-0.2051	0.4921	1.0216	0.9252	-0.2808	0.3001	0.7977	-0.1236	0.0468	0.3631	0.0232	0.5815	-49.8424	57.1684	-85.0997
17	3.9921	0.6734	-2.0804	0.1296	-0.356	3.5543	0.2535	-0.016	-0.4605	1.2368	0.2053	-1.3483	0.5555	0.3745	-0.3053	0.7597	-0.0552	-0.1404	0.3795	0.0104	0.4389	-32.7582	102.4549	-74.733
18	1.0777	-0.0196	0.3318	0.1142	-0.2354	2.4165	0.1287	-0.2092	0.083	1.6919	0.1267	0.8156	-0.2602	-0.0969	-0.2303	0.8425	-0.0141	0.1469	0.4695	-0.0616	0.3487	-62.0483	134.4533	-120.1647
19	2.4024	-0.1355	-0.7163	2.3846	-1.8333	3.1661	-0.2719	0.2445	-0.4567	0.0996	0.1434	-0.2512	0.6893	-0.4183	-0.0704	0.5007	-0.0781	0.0732	0.1698	-0.0302	0.1511	-61.009	115.715	-127.9894
20	2.0091	-0.3828	-0.5907	2.5252	1.0318	1.8831	-0.1482	-0.7453	-0.0238	0.5537	0.6147	-1.0595	-1.0147	0.0995	-0.2733	1.2862	0.0389	-0.0869	0.7086	-0.1567	1.085	-46.2414	152.7796	-129.3536
21	1.8241	0.8414	-0.8978	0.3519	-0.7071	2.2767	0.37	-0.143	0.0505	1.862	-0.5316	-1.0773	-0.4721	0.2472	0.0524	0.7742	-0.1369	-0.231	0.4751	0.0453	0.4527	-53.1696	142.7813	-121.2995
22	2.743	0.0743	0.0897	5.8226	2.563	3.2982	-0.3439	0.3354	0.6469	-0.3707	0.6782	-0.8782	-0.9549	0.429	0.2454	0.8208	-0.13	-0.0332	0.4063	0.0111	0.5921	-52.8947	161.9748	-131.2172
23	3.1279	0.9259	-0.0287	0.3955	0.0053	3.2542	0.7369	-0.1559	0.6427	1.9901	-0.007	1.7675	-1.1995	-0.4168	-0.1857	0.8304	-0.0784	0.247	0.27	0.1117	0.3402	-70.0216	116.7222	-120.8604

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 4 through 52 )	A	3 - 51
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 91 )	A	52 - 90
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 114 )	A	91 - 113
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 3 through 52 )	B	2 - 51
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 53 through 93 )	B	52 - 92
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 94 through 120 )	B	93 - 119
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 4 through 51 )	C	3 - 50
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 52 through 91 )	C	51 - 90
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 92 through 114 )	C	91 - 113
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 3 through 52 )	D	2 - 51
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 53 through 92 )	D	52 - 91
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 93 through 120 )	D	92 - 119
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 3 through 92 )	E	2 - 91
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 93 through 115 )	E	92 - 114
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 3 through 52 )	F	2 - 51
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 53 through 93 )	F	52 - 92
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 94 through 120 )	F	93 - 119
18	X-RAY DIFFRACTION	18	chain 'G' and (resid 4 through 52 )	G	3 - 51
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 53 through 91 )	G	52 - 90
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 92 through 110 )	G	91 - 109
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 3 through 52 )	H	2 - 51
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 53 through 93 )	H	52 - 92
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 94 through 120 )	H	93 - 119

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Assembly

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Experiment

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About Yorodumi

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi