PDB-3lr6: Self-assembly of spider silk proteins is controlled by a pH-sensi...

ID or keywords:

Entry

Database: PDB / ID: 3lr6

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 D40N 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: 2.2 Å

Authors

Askarieh, G. / Hedhammar, H. / Nordling, K. / Saenz, A. / Casals, C. / 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3lr6.cif.gz	104.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3lr6.ent.gz	83.8 KB	Display	PDB format
PDBx/mmJSON format	3lr6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3lr6_validation.pdf.gz	447.4 KB	Display	wwPDB validaton report
Full document	3lr6_full_validation.pdf.gz	449.4 KB	Display
Data in XML	3lr6_validation.xml.gz	12.1 KB	Display
Data in CIF	3lr6_validation.cif.gz	15.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lr/3lr6 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lr6	HTTPS FTP

-
Related structure data

Related structure data	3lr2C 3lr8C 3lrdC C: citing same article (ref.)
Similar structure data	5hd9-d 3hgn-d 2btc-d 5ms3-d 5qhg-d 3h7o-1 4cf7-2 4p92-d 4y7u-d 4qkb-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Major ampullate spidroin 1

B: Major ampullate spidroin 1

hetero molecules

28.5 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)	68.670, 68.670, 97.342
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-178- HOH

#1: Protein	Major ampullate spidroin 1 Mass: 14182.729 Da / Num. of mol.: 2 / Mutation: D40N 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-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.: 62 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.34 %
Crystal grow	Method: vapor diffusion / Details: Ammonium sulphate, PEG 400, VAPOR DIFFUSION

-
Data collection

Diffraction

ID	Crystal-ID
1	1
2	1
3	1

Diffraction source

Source	Site	Beamline	ID
SYNCHROTRON	ESRF	ID14-2	1
SYNCHROTRON	ESRF	ID23-1	2
SYNCHROTRON	ESRF	ID23-2	3

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: 2.2→59.44 Å / Num. obs: 12619 / Observed criterion σ(I): 2.2 / Redundancy: 4.5 % / B_iso Wilson estimate: 27.1 Å² / R_merge(I) obs: 0.089 / Net I/σ(I): 7.4

Reflection shell

Resolution: 2.2→2.257 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.345 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1538

-
Processing

Software

Name: REFMAC / Version: 5.2.0019 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→59.4 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.919 / SU B: 12.908 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24794	664	5 %	RANDOM
R_work	0.20737	-	-	-
obs	0.20929	12619	95.17 %	-

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: 13.122 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.63 Å²	0.31 Å²	0 Å²
2-	-	0.63 Å²	0 Å²
3-	-	-	-0.94 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→59.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1852	0	10	62	1924

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	1911
X-RAY DIFFRACTION	r_angle_refined_deg	1.333	1.94	2596
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.872	5	266
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.936	26.986	73
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.142	15	319
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.885	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	305
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1424
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	967
X-RAY DIFFRACTION	r_nbtor_refined	0.291	0.2	1385
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	72
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.252	0.2	41
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.225	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	6.865	1.5	1312
X-RAY DIFFRACTION	r_mcangle_it	6.449	2	2048
X-RAY DIFFRACTION	r_scbond_it	8.09	3	673
X-RAY DIFFRACTION	r_scangle_it	7.793	4.5	540

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.322	41	-
R_work	0.251	698	-
obs	-	-	73.75 %

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	30.7822	-7.7957	2.634	9.1144	10.0735	16.382	-0.1636	0.1791	1.1195	-0.2803	0.3954	0.3544	-0.399	-0.7503	-0.2317	0.1293	-0.0328	0.0151	0.092	0.0301	0.0913	20.1198	-9.6916	22.5488
2	0.5906	-1.6828	0.2797	8.069	-2.7035	1.2426	-0.0341	-0.0461	0.0451	-0.0271	0.0039	-0.2442	-0.0042	-0.0522	0.0302	0.081	-0.0233	-0.0108	0.1455	0.0029	0.0279	26.6886	-17.5795	22.9208
3	10.7705	-2.933	3.4403	33.8074	2.0433	18.635	0.407	-0.2846	-0.3337	0.4765	-0.8003	-0.9676	-0.8061	0.1436	0.3934	0.071	-0.0022	-0.011	0.0605	0.0031	0.0849	27.7532	-30.4895	28.9664
4	1.1893	2.4708	-0.3936	6.0044	0.6274	2.527	-0.051	0.021	-0.1894	-0.2092	0.0747	-0.3071	0.0991	0.1543	-0.0236	0.0551	0.0127	0.0281	0.1243	0.01	0.0619	28.6076	-34.2589	19.6861
5	0.9065	0.8815	-1.0338	24.3195	-3.8354	1.5203	-0.0347	0.137	-0.0652	-0.4463	-0.1289	-0.3466	0.2081	0.4287	0.1636	0.1092	-0.0076	0.0224	0.1024	0.0117	0.068	31.7731	-15.2584	13.4883
6	0.3185	1.6695	-0.795	15.3637	-3.71	2.0156	0.0435	-0.0431	0.0393	-0.0073	-0.128	0.0553	-0.0202	-0.0679	0.0844	0.0791	0.0016	-0.0268	0.1422	-0.0045	0.0733	21.2032	-19.5852	14.2515
7	8.0106	-2.6436	-3.8317	7.634	-1.6461	3.0857	0.1067	0.4089	-0.378	-0.2918	0.007	0.3621	0.6537	-0.4668	-0.1137	0.131	-0.0797	-0.0279	0.094	-0.0113	0.04	19.497	-40.4759	19.1443
8	0.5412	1.2362	0.3558	3.1699	1.2126	0.6955	-0.0606	0.0863	-0.0659	-0.1008	0.1834	-0.1547	0.0589	0.1016	-0.1228	0.0661	-0.0077	0.004	0.1304	0.0088	0.0514	17.9782	-23.7537	27.7259
9	12.3456	-6.0634	-3.1867	15.1518	11.6998	9.2597	-0.4464	-0.1302	0.4469	-0.4688	0.3923	-0.1772	-0.1791	0.0116	0.0542	0.0242	-0.0745	0.0663	0.1293	0.0432	0.0619	12.0688	-28.2206	19.1643
10	29.2566	-1.706	-2.128	30.8738	30.9576	31.0477	-0.7575	1.404	-0.5974	-1.3043	-0.0539	1.4517	0.7837	-1.227	0.8114	0.1424	-0.143	0.0306	0.1094	-0.0453	0.0461	11.3713	-35.0297	13.3671
11	24.6247	7.0305	9.3333	11.7751	5.6556	24.5884	0.0874	0.2868	-1.5818	-0.2152	-0.2098	-0.0075	1.8678	0.1943	0.1224	0.2451	0.0194	0.0794	0.1068	-0.0193	0.1565	23.1429	-37.6298	-0.398
12	6.1359	-7.2141	0.3732	8.7221	0.4492	3.3023	-0.154	-0.0664	0.0122	-0.1607	-0.0048	-0.179	-0.1592	0.1792	0.1589	0.0942	-0.0735	-0.0002	0.1155	-0.0004	0.0479	26.0894	-27.133	-1.8214
13	34.7822	-9.1483	-15.1199	18.539	-5.7446	19.7356	0.1453	2.0836	1.9679	-0.5315	-0.1267	-0.4124	-1.2869	-0.0482	-0.0186	0.15	-0.0057	-0.003	0.095	0.0158	0.1028	17.0966	-16.93	-5.9964
14	32.8566	5.3519	6.0642	12.1679	6.8307	8.1047	-0.8938	-0.8835	1.2471	-0.9837	0.4052	0.1435	-0.923	-0.4625	0.4886	0.1901	0.1192	-0.1095	0.0306	0.0561	-0.0578	14.2268	-10.6347	0.3257
15	2.2636	-1.9537	-0.499	2.833	-0.1397	0.6268	-0.0155	-0.063	0.044	-0.0418	-0.0042	-0.1427	-0.1273	0.064	0.0198	0.1054	-0.0134	0.0049	0.1182	-0.0058	0.0324	29.9535	-25.1743	6.3432
16	6.0237	-8.5305	0.4644	12.5272	0.2221	1.7684	-0.1131	-0.0373	0.0353	0.0234	-0.146	0.0581	-0.0544	-0.142	0.2591	0.0762	0.0129	-0.01	0.1911	0.0203	0.0411	17.359	-21.8344	7.189
17	12.2731	13.2178	10.0069	14.2789	9.9469	23.9434	0.0128	-0.4082	0.4727	-0.003	0.0822	0.8382	-0.6563	-0.622	-0.095	0.0553	0.2636	-0.03	0.2099	-0.114	0.1043	6.6307	-12.8211	4.5398
18	8.4237	-6.5508	-2.251	8.2804	4.2137	2.5058	-0.0653	0.4229	-0.1892	-0.1716	0.0745	0.027	-0.2141	-0.4086	-0.0092	0.0988	0.001	-0.0477	0.1635	-0.0077	0.0419	13.7749	-24.6444	-4.0507
19	2.7091	-2.8394	-3.5257	4.6912	5.7248	10.2919	-0.362	-0.1036	-0.1797	0.4862	0.0273	0.3585	0.9691	-0.2825	0.3347	0.0288	-0.06	-0.0113	0.1471	0.0219	0.0567	12.091	-28.9666	3.4937
20	37.003	25.4252	18.4327	52.9434	2.4733	13.9897	-0.1212	-3.8304	2.3351	3.2874	-1.8748	-0.7198	-1.863	-2.3247	1.9959	0.5273	0.0735	-0.1499	0.491	-0.2101	0.3133	9.5874	-15.3258	19.8336

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 10
2	X-RAY DIFFRACTION	2	A	11 - 24
3	X-RAY DIFFRACTION	3	A	25 - 30
4	X-RAY DIFFRACTION	4	A	31 - 45
5	X-RAY DIFFRACTION	5	A	46 - 59
6	X-RAY DIFFRACTION	6	A	60 - 81
7	X-RAY DIFFRACTION	7	A	82 - 91
8	X-RAY DIFFRACTION	8	A	92 - 118
9	X-RAY DIFFRACTION	9	A	119 - 124
10	X-RAY DIFFRACTION	10	A	125 - 130
11	X-RAY DIFFRACTION	11	B	5 - 10
12	X-RAY DIFFRACTION	12	B	11 - 23
13	X-RAY DIFFRACTION	13	B	24 - 30
14	X-RAY DIFFRACTION	14	B	31 - 39
15	X-RAY DIFFRACTION	15	B	40 - 69
16	X-RAY DIFFRACTION	16	B	70 - 82
17	X-RAY DIFFRACTION	17	B	83 - 92
18	X-RAY DIFFRACTION	18	B	93 - 107
19	X-RAY DIFFRACTION	19	B	108 - 128
20	X-RAY DIFFRACTION	20	B	129 - 135

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi