PDB-3lr8: Self-assembly of spider silk proteins is controlled by a pH-sensi...

ID or keywords:

Entry

Database: PDB / ID: 3lr8

Title

Self-assembly of spider silk proteins is controlled by a pH-sensitive relay

Components

Major ampullate spidroin 1

Keywords

STRUCTURAL PROTEIN / dragline spider silk /

self-assembly / pH-dependence / NT E79Q mutant

Function / homology

Function and homology information

identical protein binding
Similarity search - Function

Biological species

Euprosthenops australis (spider)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Askarieh, G. / Hedhammar, H. / Nordling, K. / Rising, A. / Johansson, J. / Knight, S.D.

Citation

Journal: Nature / Year: 2010
Title: Self-assembly of spider silk proteins is controlled by a pH-sensitive relay.
Authors: Askarieh, G. / Hedhammar, M. / Nordling, K. / Saenz, A. / Casals, C. / Rising, A. / Johansson, J. / Knight, S.D.

History

Deposition	Feb 10, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 12, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 13, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lr8.cif.gz	108.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3lr8.ent.gz	86.3 KB	Display	PDB format
PDBx/mmJSON format	3lr8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lr/3lr8 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lr8	HTTPS FTP

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Related structure data

Related structure data	3lr2C 3lr6C 3lrdC C: citing same article (ref.)
Similar structure data	6v3t-6 5brl-1 1tf8-d 6d4g-1 6st3-1 2wfm-4 2wfl-2 5hd9-d 4mkg-d 3c5h-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Major ampullate spidroin 1

B: Major ampullate spidroin 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	91.193, 91.193, 143.546
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-153- HOH
2	1	B-171- HOH

#1: Protein	Major ampullate spidroin 1 Mass: 14182.728 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: E79Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Euprosthenops australis (spider) / Gene: MaSp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05H60
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.04 Å³/Da / Density % sol: 59.5 %
Crystal grow	Method: vapor diffusion / Details: Ammonium sulphate, PEG 400, VAPOR DIFFUSION

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Data collection

Diffraction

ID	Crystal-ID
1	1
2	1

Diffraction source

Source	Site	Beamline	ID
SYNCHROTRON	ESRF	ID23-1	1
SYNCHROTRON	ESRF	ID14-4	2

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

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

Radiation wavelength

Relative weight: 1

Reflection

Resolution: 2.3→79.06 Å / Num. obs: 15139 / Observed criterion σ(I): 2.2 / Redundancy: 11.4 % / R_merge(I) obs: 0.144 / Net I/σ(I): 2

Reflection shell

Resolution: 2.3→2.36 Å / Redundancy: 11.9 % / R_merge(I) obs: 0.341 / Mean I/σ(I) obs: 7.8 / Num. unique all: 2315

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Processing

Software

Name: REFMAC / Version: 5.2.0019 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NT wild-type

Resolution: 2.3→53.1 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.883 / SU B: 10.794 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24654	808	5.1 %	RANDOM
R_work	0.19156	-	-	-
obs	0.19436	15139	97.72 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 8.444 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.59 Å²	0.3 Å²	0 Å²
2-	-	0.59 Å²	0 Å²
3-	-	-	-0.89 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→53.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1850	0	50	97	1997

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	2003
X-RAY DIFFRACTION	r_angle_refined_deg	1.487	1.954	2718
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	10.141	5	292
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.552	27.123	73
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.79	15	331
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.671	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	317
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1482
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	1028
X-RAY DIFFRACTION	r_nbtor_refined	0.29	0.2	1404
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	100
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.192	0.2	44
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.148	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.99	1.5	1362
X-RAY DIFFRACTION	r_mcangle_it	1.079	2	2136
X-RAY DIFFRACTION	r_scbond_it	2.372	3	716
X-RAY DIFFRACTION	r_scangle_it	3.267	4.5	563

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.223	63	-
R_work	0.165	1114	-
obs	-	-	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	9.8838	3.1625	-3.1217	1.0754	-2.089	19.698	-0.426	0.1021	-0.954	-0.336	0.1733	-0.0679	0.4788	-0.7217	0.2527	0.1364	-0.0662	0.029	0.0086	-0.0203	0.1029	9.3297	-39.7852	-26.0023
2	9.1656	-2.6404	-4.2915	0.7618	1.2894	4.3199	0.0074	0.1819	-0.088	0.0261	0.025	0.046	-0.114	-0.0096	-0.0324	0.0429	-0.019	-0.0343	0.0736	0.0251	0.0529	4.7226	-31.269	-17.9199
3	6.0427	1.8025	0.8434	2.5508	1.1033	5.0809	-0.09	-0.1832	0.4729	-0.2237	-0.1029	0.2302	-0.3194	-0.0588	0.1929	0.052	0.0213	-0.011	0.0591	-0.0128	0.0597	-5.4807	-25.0166	-5.5431
4	5.6972	-2.4356	-4.0712	1.0455	1.6658	4.2403	-0.0316	-0.1584	0.2351	0.0297	0.1267	-0.0915	-0.127	0.1256	-0.0951	0.0675	-0.0277	-0.0325	0.0792	0.0092	0.0401	10.2043	-25.2978	-12.672
5	4.0987	-0.34	-2.57	0.3187	-0.0262	2.1927	-0.1909	-0.1161	-0.1101	-0.083	0.1529	0.1276	0.1356	0.1331	0.038	0.072	-0.0049	-0.0466	0.0605	-0.0039	0.0163	15.6452	-36.1017	-15.1191
6	4.4188	-0.6103	-4.0519	2.5525	3.5481	14.8142	-0.0351	-0.2259	0.1987	0.1254	-0.1143	0.2144	-0.2344	-0.1219	0.1495	0.002	0.0057	-0.0478	0.0831	0.0152	0.0576	3.6225	-32.2116	-2.7527
7	2.2388	3.3637	1.4749	5.054	2.216	0.9717	0.0273	-0.5359	-0.0271	0.2782	-0.1035	-0.0749	0.321	0.0396	0.0762	0.0136	0.0076	-0.0117	0.2164	0.0102	0.0861	-4.9357	-29.6389	4.6531
8	0.3906	0.1823	-0.3694	1.6043	0.4109	4.8016	0.1524	0.0037	0.0082	-0.0855	0.0616	-0.0102	0.3435	-0.0015	-0.2139	-0.0248	-0.0007	-0.023	0.066	0.0139	0.081	-5.6278	-35.5046	-8.7825
9	3.2794	-0.2076	2.4547	6.6315	-8.3547	11.9954	0.3658	0.1935	-0.3685	-0.4538	-0.0363	0.1678	0.7992	0.1763	-0.3295	0.1158	0.0331	-0.044	0.0426	-0.0078	0.0588	-1.405	-41.4373	-15.6576
10	8.7756	-1.2652	4.0001	7.6379	3.2615	16.9142	0.0247	-0.5761	-0.4539	0.263	-0.1744	0.2308	0.3849	-0.2552	0.1497	0.0202	-0.0661	0.0354	0.0753	0.0616	0.0624	1.7525	-40.1614	1.5489
11	15.5115	-0.398	3.6075	9.1045	-13.9927	22.0844	0.4464	-0.4665	-0.135	0.1183	0.489	0.9349	0.2274	-1.2355	-0.9354	0.1119	-0.0488	-0.0752	0.1245	-0.0166	0.0167	14.9468	-25.9974	8.4422
12	2.8285	-2.0999	0.3363	8.5837	0.9205	1.0095	0.0727	0.0029	0.0854	-0.1637	-0.0133	-0.3193	-0.1428	0.0144	-0.0594	0.0228	-0.0193	-0.0182	0.0569	0.0155	0.0064	23.427	-30.188	1.3906
13	1.4877	-1.0207	0.835	3.5452	-2.9721	2.492	-0.0458	0.1735	0.0176	-0.0926	-0.1076	-0.0761	0.1857	0.2094	0.1534	0.0354	0.0085	-0.0072	0.1043	0.0033	0.0244	25.9954	-39.9314	-7.1969
14	5.9479	-7.1077	-1.7645	13.7858	1.994	3.3391	0.0148	0.2407	0.3164	-0.2602	0.0549	0.1175	-0.0841	-0.1044	-0.0697	0.0499	-0.0402	-0.0428	0.0961	0.0194	0.0395	16.991	-21.7229	-6.2129
15	1.9675	-3.1688	-0.1579	9.1431	0.5873	0.0424	0.0438	-0.0004	0.1167	0.1082	-0.1314	-0.1166	-0.1062	-0.1721	0.0875	0.0248	-0.0145	-0.0472	0.0818	0.0099	0.0521	10.7055	-27.6352	-0.3417
16	1.4832	-1.9346	0.9276	3.5173	-0.2791	1.4519	0.1716	0.2339	-0.1452	-0.1963	-0.0218	-0.0854	0.1549	-0.0423	-0.1498	0.0611	0.0013	-0.0169	0.0675	0.0028	0.0924	19.0076	-46.9983	-6.2554
17	0.6269	-1.5123	-0.6698	3.6516	1.6538	1.1136	-0.0896	0.0662	-0.133	0.0473	0.1376	0.0233	0.0755	0.0954	-0.048	0.0404	-0.0065	-0.0082	0.0182	0.0135	0.0537	22.2298	-40.9814	5.0743
18	8.7642	7.1745	3.6136	7.1379	0.9573	5.5725	0.215	-0.374	0.0051	0.2695	-0.1448	-0.0763	0.201	-0.0663	-0.0701	-0.0123	0.0243	0.0024	0.0407	-0.0116	0.0572	18.0097	-34.0489	11.2693
19	7.0459	2.6295	2.3835	16.825	0.6532	10.9237	0.2274	-0.1753	0.3244	-0.3976	0.1376	-0.3571	0.1877	-0.3286	-0.365	-0.0617	-0.0183	-0.0101	0.0044	0.0274	0.0662	13.1008	-42.2407	5.7548
20	8.8196	4.5176	7.2126	15.2241	8.4488	14.3822	-0.0536	0.157	-0.9614	-0.1465	0.0937	0.5906	0.899	-0.5325	-0.04	0.1106	-0.0442	-0.0305	-0.0191	0.0467	0.1109	9.9678	-49.0963	-4.1219

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 10
2	X-RAY DIFFRACTION	2	A	11 - 24
3	X-RAY DIFFRACTION	3	A	25 - 40
4	X-RAY DIFFRACTION	4	A	41 - 57
5	X-RAY DIFFRACTION	5	A	58 - 72
6	X-RAY DIFFRACTION	6	A	73 - 82
7	X-RAY DIFFRACTION	7	A	83 - 90
8	X-RAY DIFFRACTION	8	A	91 - 106
9	X-RAY DIFFRACTION	9	A	107 - 118
10	X-RAY DIFFRACTION	10	A	119 - 131
11	X-RAY DIFFRACTION	11	B	7 - 12
12	X-RAY DIFFRACTION	12	B	13 - 27
13	X-RAY DIFFRACTION	13	B	28 - 45
14	X-RAY DIFFRACTION	14	B	46 - 59
15	X-RAY DIFFRACTION	15	B	60 - 76
16	X-RAY DIFFRACTION	16	B	77 - 91
17	X-RAY DIFFRACTION	17	B	92 - 106
18	X-RAY DIFFRACTION	18	B	107 - 116
19	X-RAY DIFFRACTION	19	B	117 - 121
20	X-RAY DIFFRACTION	20	B	122 - 133

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