PDB-6r9d: Crystal structure of an asymmetric dimer of the N-terminal domain...

ID or keywords:

Entry

Database: PDB / ID: 6r9d

Title

Crystal structure of an asymmetric dimer of the N-terminal domain of Euprosthenops australis Major Ampullate Spidroin 1 (dragline silk)

Components

Major ampullate spidroin 1

Keywords

PROTEIN FIBRIL / Spider silk Spidroin N-terminal domain pH relay Assembly

Function / homology

Spidroin, N-terminal domain / Spidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha / identical protein binding / Major ampullate spidroin 1

Function and homology information

Biological species

Euprosthenops australis (spider)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Knight, S.D. / Jiang, W. / Askarieh, G.

Funding support

Sweden, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structure of the N-terminal domain of Euprosthenops australis dragline silk suggests that conversion of spidroin dope to spider silk involves a conserved asymmetric dimer intermediate.
Authors: Jiang, W. / Askarieh, G. / Shkumatov, A. / Hedhammar, M. / Knight, S.D.

History

Deposition	Apr 3, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 17, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6r9d.cif.gz	399.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6r9d.ent.gz	340.5 KB	Display	PDB format
PDBx/mmJSON format	6r9d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6r9d_validation.pdf.gz	475.1 KB	Display	wwPDB validaton report
Full document	6r9d_full_validation.pdf.gz	478.3 KB	Display
Data in XML	6r9d_validation.xml.gz	27.5 KB	Display
Data in CIF	6r9d_validation.cif.gz	38.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r9/6r9d ftp://data.pdbj.org/pub/pdb/validation_reports/r9/6r9d	HTTPS FTP

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Related structure data

Related structure data	3lr2S S: Starting model for refinement
Similar structure data	3lr2-d 3lrd-d 1uu4-d 2icu-1 1h9i-d 4jl5-2 4ff5-d 4eyf-2 2pbl-4 1j08-1 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

3lr2S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Major ampullate spidroin 1

B: Major ampullate spidroin 1

C: Major ampullate spidroin 1

D: Major ampullate spidroin 1

E: Major ampullate spidroin 1

F: Major ampullate spidroin 1

hetero molecules

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

1

A: Major ampullate spidroin 1

B: Major ampullate spidroin 1

defined by author&software
Evidence: gel filtration, SAXS also supports the dimer to be the functional assembly
28.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Major ampullate spidroin 1

D: Major ampullate spidroin 1

defined by author&software
Evidence: gel filtration, SAXS also supports the dimer to be the functional assembly
28.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Major ampullate spidroin 1

F: Major ampullate spidroin 1

hetero molecules

defined by author&software
Evidence: gel filtration, SAXS also supports the dimer to be the functional assembly
28.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	126.631, 65.114, 95.968
Angle α, β, γ (deg.)	90.00, 91.85, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-31- PRO

#1: Protein	Major ampullate spidroin 1 Mass: 14153.687 Da / Num. of mol.: 6 / Mutation: T61A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Euprosthenops australis (spider) / Gene: MaSp1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05H60
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.33 Å³/Da / Density % sol: 47.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 15% PEG 3350 1 M Ammonium sulphate 0.1 M Tris-HCl buffer pH 8.5 15% PEG 400 PH range: 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 11, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9334 Å / Relative weight: 1
Reflection	Resolution: 2.1→57.9 Å / Num. obs: 45467 / % possible obs: 99.27 % / Redundancy: 4.8 % / B_iso Wilson estimate: 31.79 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.195 / R_pim(I) all: 0.085 / R_rim(I) all: 0.213 / Net I/σ(I): 10.16
Reflection shell	Resolution: 2.1→2.175 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.422 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 4464 / CC_1/2: 0.795 / R_pim(I) all: 0.364 / R_rim(I) all: 0.559 / % possible all: 98.13

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LR2

3lr2

Resolution: 2.1→57.9 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.33

	R_factor	Num. reflection	% reflection
R_free	0.2369	2391	5.26 %
R_work	0.2078	-	-
obs	0.2093	45463	99.27 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→57.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5398	0	5	177	5580

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5627
X-RAY DIFFRACTION	f_angle_d	0.453	7638
X-RAY DIFFRACTION	f_dihedral_angle_d	8.371	3448
X-RAY DIFFRACTION	f_chiral_restr	0.034	889
X-RAY DIFFRACTION	f_plane_restr	0.004	1015

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 (%)
2.1-2.1429	0.3426	146	0.295	2466	X-RAY DIFFRACTION	98
2.1429-2.1895	0.2784	133	0.285	2485	X-RAY DIFFRACTION	98
2.1895-2.2404	0.2968	149	0.2562	2495	X-RAY DIFFRACTION	98
2.2404-2.2964	0.303	133	0.2586	2493	X-RAY DIFFRACTION	98
2.2964-2.3585	0.3058	148	0.2381	2467	X-RAY DIFFRACTION	98
2.3585-2.4279	0.2807	130	0.2398	2506	X-RAY DIFFRACTION	98
2.4279-2.5063	0.2989	122	0.231	2529	X-RAY DIFFRACTION	99
2.5063-2.5959	0.2666	131	0.2164	2552	X-RAY DIFFRACTION	100
2.5959-2.6998	0.2887	124	0.2221	2547	X-RAY DIFFRACTION	100
2.6998-2.8227	0.2432	159	0.2219	2548	X-RAY DIFFRACTION	100
2.8227-2.9715	0.277	126	0.2133	2577	X-RAY DIFFRACTION	100
2.9715-3.1577	0.2493	155	0.2222	2502	X-RAY DIFFRACTION	100
3.1577-3.4015	0.2233	149	0.2139	2565	X-RAY DIFFRACTION	100
3.4015-3.7437	0.223	132	0.1891	2574	X-RAY DIFFRACTION	100
3.7437-4.2854	0.1996	130	0.17	2563	X-RAY DIFFRACTION	100
4.2854-5.3987	0.189	151	0.1758	2589	X-RAY DIFFRACTION	100
5.3987-57.9	0.2079	173	0.1983	2614	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	2.2886	-0.3605	0.027	0.067	-0.2549	5.9004	-0.0836	-0.3532	0.56	0.3959	-0.2904	-0.8153	-1.2905	0.0551	0.0578	0.2351	-0.0219	-0.0794	0.3457	0.0244	0.3549	53.7883	43.4775	5.7227
2	1.177	0.2053	0.4054	0.7901	-0.1455	0.4519	-0.2236	0.0418	-0.5219	0.0698	0.0282	0.1911	0.113	-0.1994	-0.0064	0.1602	-0.0012	-0.0183	0.2714	-0.0088	0.33	38.9296	35.3675	4.3647
3	0.3505	-0.1147	0.1018	0.8212	-0.1397	0.7739	0.1384	0.3175	0.1999	0.0035	-0.0863	-0.0204	-0.2068	-0.0648	0.0014	0.1815	-0.0059	-0.0502	0.2949	-0.0242	0.3297	42.4816	42.8142	-2.3348
4	0.3082	0.3204	-0.1567	0.9847	0.9634	2.0368	0.141	0.1228	-0.1242	-0.1368	0.0975	0.3708	0.0398	-0.2137	1.6201	0.1782	0.0784	-0.1833	0.6948	0.0945	0.4743	21.2915	42.0186	3.4766
5	0.388	0.2092	-0.2585	0.8609	0.0935	0.4324	-0.2365	0.1591	-0.2495	0.1573	0.1251	0.0442	-0.0377	0.0405	-0	0.2176	0.0768	-0.0231	0.3029	0.0422	0.3548	37.5201	45.5349	11.7987
6	0.81	0.2442	0.1763	0.614	-0.6492	0.9398	0.0008	0.267	0.2078	-0.052	-0.099	0.0756	-0.7174	0.0705	0.0325	0.2967	0.0997	-0.0586	0.2685	0.0246	0.3129	33.8516	51.8857	2.179
7	0.1024	0.1862	-0.2167	0.3483	-0.4034	0.4666	-0.544	0.313	0.3936	-0.4512	0.021	0.5148	-0.2032	-0.5921	-0.4173	0.2971	0.0137	-0.1526	0.5127	-0.1	0.4498	27.0679	36.7741	-15.8157
8	0.256	-0.099	0.1781	0.368	0.2312	0.4402	-0.1304	0.3052	-0.3204	-0.4756	0.0315	-0.4554	-0.2006	0.1465	0.0008	0.3249	-0.0228	-0.0276	0.2718	-0.0382	0.3754	39.5226	39.361	-19.7007
9	1.2547	0.562	-0.0704	0.6568	-0	0.0071	-0.0755	0.129	0.1416	-0.2486	-0.1013	-0.2446	0.0633	0.1157	-0.4862	0.5541	-0.4247	0.2174	0.1892	0.1961	0.3477	48.4704	51.9283	-20.2896
10	1.123	-0.4643	0.538	0.9604	0.3837	1.0282	-0.0764	-0.0692	0.0405	-0.1309	-0.0426	-0.1641	-0.0007	0.4785	-0.0132	0.2168	-0.0708	-0.0065	0.3143	-0.051	0.3351	44.8014	35.9239	-11.8806
11	0.4435	-0.5504	0.3675	0.687	-0.4654	0.4872	0.1452	-0.1663	0.1016	-0.051	-0.238	0.066	-0.2509	-0.1434	0.0007	0.2546	-0.0027	-0.0439	0.2559	-0.0206	0.3077	36.7386	40.6806	-8.2843
12	1.4644	-0.6055	-0.8546	1.0808	0.2517	0.5508	0.2634	-0.2201	0.2441	0.0974	0.1306	-0.3918	-0.4391	0.2898	0.1663	0.6235	-0.248	-0.1437	0.4116	0.0805	0.6184	52.0571	55.6804	-12.9187
13	0.7189	-0.2897	0.4312	0.3526	0.4524	1.8157	0.1892	0.4271	0.2604	-0.637	-0.1457	-0.071	-0.7574	-0.125	0.0014	0.331	0.0568	-0.1252	0.3083	-0.0199	0.3889	35.8953	48.4845	-20.3444
14	2.1941	0.2437	-0.2639	0.5359	-0.8186	1.275	-0.1413	-0.0153	0.874	-0.2374	-0.3088	0.3117	-0.9854	-0.2951	-0.0219	0.4102	0.1119	-0.1322	0.2362	-0.0424	0.3972	36.0776	54.0005	-8.6454
15	1.1966	-0.6363	0.6464	0.7052	-0.2702	0.3181	0.0766	-0.6349	0.4734	0.4351	0.0207	-0.1612	-0.1523	0.132	0.0068	0.8788	-0.0724	0.1934	0.6514	-0.0959	0.5008	50.8062	26.5995	39.96
16	1.4652	0.3998	1.4338	1.053	0.074	1.3336	0.0314	-0.0329	0.4861	0.2852	-0.1204	0.0448	-0.3421	0.4128	-0.0001	0.6447	-0.0582	0.0748	0.5872	0.025	0.5142	56.1164	27.4591	34.8581
17	1.1308	-0.7132	0.5264	0.5537	-0.4374	1.417	-0.5186	-0.3241	-0.6909	0.147	0.3054	0.0428	0.4341	0.042	-0.0071	0.3315	0.0748	0.0778	0.4107	0.0928	0.4593	55.841	30.8449	13.4694
18	0.6115	-0.7351	0.2961	1.0459	-0.12	0.3593	-0.1691	-0.0749	-0.6994	-0.0465	0.2095	0.701	0.3485	-0.1247	0.1072	0.6013	0.34	0.2813	0.4042	0.3029	0.7924	50.3263	23.2564	18.8311
19	0.6868	0.1618	0.6126	0.0434	0.1403	0.5416	-0.6602	-0.8706	-0.4112	0.567	0.1638	0.1028	0.0218	0.3671	-0.046	0.6973	0.3407	0.1272	0.7618	0.1821	0.5047	56.5988	29.6912	23.9435
20	0.7245	0.3264	0.5891	0.8619	-0.3269	0.9566	-0.5724	-0.0895	-0.5301	0.1449	0.1608	-0.0221	0.5795	0.4915	-0.1458	0.4107	0.225	0.1793	0.4645	0.1326	0.4565	63.2229	22.0266	13.6853
21	0.2809	-0.5281	0.7467	1.2311	-1.2869	2.0554	-0.513	-0.4993	-0.4957	0.9475	0.0289	-0.7823	-0.0778	0.6352	-0.0473	0.5014	0.2652	0.0318	0.7873	0.1665	0.5808	67.8049	22.9037	23.574
22	0.7135	-0.1668	0.3874	1.6613	-0.1253	1.7008	0.0803	-0.0637	0.2831	0.5196	-0.1598	0.4573	0.1041	-0.1629	-0.0002	0.4284	0.0413	0.0852	0.4385	-0.0098	0.3836	24.5201	55.0792	27.7576
23	1.8409	0.0727	-0.2806	1.0074	0.1102	1.9186	-0.1326	-0.3891	-0.3079	0.5524	-0.0866	0.0053	0.4509	0.1353	-0.0074	0.4518	0.1009	0.0283	0.3131	0.0919	0.3232	30.4043	46.8068	26.9536
24	0.0289	-0.0145	0.0145	0.0313	0.0131	0.0327	0.3168	-0.2629	-0.8667	-0.0302	-0.0443	-0.3292	0.2827	-0.2138	-0.0002	0.789	0.1392	0.1451	0.5669	0.0696	0.5451	17.9726	43.1827	48.2657
25	0.5815	-0.3612	0.1132	0.7053	0.1606	0.4451	0.1295	-0.3399	0.0918	0.3926	-0.104	0.2075	-0.6393	0.222	0.0362	1.0075	0.0901	0.1409	0.527	0.0904	0.2661	26.0963	53.3731	51.2499
26	0.7932	-0.1998	-0.4639	1.1457	-0.5788	1.115	-0.2373	-0.1589	0.0673	0.5619	0.1488	-0.0444	-0.7681	0.2104	-0.0155	0.8787	0.0667	0.0772	0.4954	0.0255	0.3398	25.8023	57.9211	44.2448
27	0.9582	-0.7492	-0.0231	1.3853	-0.1002	1.5568	0.0468	-0.1703	-0.4539	0.5152	-0.0971	-0.4136	-0.282	0.2924	0.0059	0.6262	0.0949	0.0102	0.4827	0.0722	0.375	31.2874	50.7906	40.8775
28	0.3864	0.4584	0.2302	1.8542	1.5002	1.2856	-0.0571	0.0274	0.1007	0.6703	0.2597	-0.2928	-0.4288	0.6105	0.2781	0.9278	0.0918	0.0195	0.628	0.1194	0.3802	34.5515	47.3713	51.4222
29	0.0464	-0.0633	0.0252	0.2874	-0.026	0.097	-0.1531	0.3186	-0.2847	0.3701	0.0683	-0.4311	0.5783	-0.5345	0.0007	0.6708	0.1385	0.119	0.5834	0.0576	0.4806	32.3286	40.9925	44.6358

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 89 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 90 through 113 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 114 through 131 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 6 through 12 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 13 through 29 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 30 through 34 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 35 through 58 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 59 through 83 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 84 through 89 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 90 through 113 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 114 through 131 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 6 through 34 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 35 through 129 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 6 through 29 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 30 through 58 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 59 through 83 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 84 through 113 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 114 through 129 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 6 through 58 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 59 through 129 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 6 through 12 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 13 through 29 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 30 through 62 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 63 through 89 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 90 through 108 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 109 through 126 )

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