PDB-6s9p: Designed Armadillo Repeat protein internal Lock2 fused to target ...

ID or keywords:

Entry

Database: PDB / ID: 6s9p

Title

Designed Armadillo Repeat protein internal Lock2 fused to target peptide KRKAKITWKR

Components

internal Lock2 fused to target peptide KRKAKITWKR

Keywords

DE NOVO PROTEIN / peptide binder / repeat protein / designed armadillo repeat protein

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Ernst, P. / Zosel, F. / Reichen, C. / Schuler, B. / Pluckthun, A.

Citation

Journal: Acs Chem.Biol. / Year: 2020
Title: Structure-Guided Design of a Peptide Lock for Modular Peptide Binders.
Authors: Ernst, P. / Zosel, F. / Reichen, C. / Nettels, D. / Schuler, B. / Pluckthun, A.

History

Deposition	Jul 15, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Mar 11, 2020	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6s9p.cif.gz	255.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6s9p.ent.gz	209 KB	Display	PDB format
PDBx/mmJSON format	6s9p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s9/6s9p ftp://data.pdbj.org/pub/pdb/validation_reports/s9/6s9p	HTTPS FTP

-
Related structure data

Related structure data	6s9lC 6s9mC 6s9nC 6s9oC C: citing same article (ref.)
Similar structure data	2x58-1 1bsz-d 3zwc-1 2ai8-d 5mgb-1 1bs8-d 1g2a-d 5j6a-1 1bs7-d 6z5v-1 Search similar-shape structures by Omokage search (details)

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: internal Lock2 fused to target peptide KRKAKITWKR

B: internal Lock2 fused to target peptide KRKAKITWKR

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: assay for oligomerization, fluorescence anisotropy measurements

Unit cell

Length a, b, c (Å)	140.680, 37.410, 127.320
Angle α, β, γ (deg.)	90.000, 96.590, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	internal Lock2 fused to target peptide KRKAKITWKR Mass: 35829.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.14 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion Details: 22.5 % PEG smear medium 0.1 M CaCl2, 0.1 M MgCl2, 0.1 M Pipes pH 7

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 1.000031 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2018

Radiation

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

Radiation wavelength

Wavelength: 1.000031 Å / Relative weight: 1

Reflection

Resolution: 2.8→44.43 Å / Num. obs: 16545 / % possible obs: 98.6 % / Redundancy: 6.662 % / B_iso Wilson estimate: 50.44 Å² / CC_1/2: 0.991 / R_merge(I) obs: 0.3 / R_rim(I) all: 0.325 / Χ²: 0.787 / Net I/σ(I): 7.12

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.8-2.87	5.918	1.815	1.27	6900	1230	1166	0.556	1.987	94.8
2.87-2.95	6.85	1.403	1.74	8069	1185	1178	0.72	1.517	99.4
2.95-3.04	7.153	1.192	2.09	8240	1158	1152	0.788	1.284	99.5
3.04-3.13	7.155	1.113	2.4	8107	1138	1133	0.812	1.199	99.6
3.13-3.23	7.101	0.955	2.82	7570	1069	1066	0.844	1.029	99.7
3.23-3.35	7.004	0.786	3.27	7564	1082	1080	0.881	0.848	99.8
3.35-3.47	6.961	0.677	3.76	7031	1017	1010	0.92	0.731	99.3
3.47-3.61	6.809	0.573	4.74	6509	959	956	0.941	0.621	99.7
3.61-3.78	6.758	0.444	6.48	6521	975	965	0.957	0.481	99
3.78-3.96	6.584	0.317	8.08	5794	889	880	0.976	0.344	99
3.96-4.17	6.534	0.29	8.74	5737	882	878	0.975	0.316	99.5
4.17-4.43	6.452	0.211	10.61	5129	805	795	0.983	0.23	98.8
4.43-4.73	6.265	0.188	11.09	4862	786	776	0.984	0.205	98.7
4.73-5.11	6.028	0.212	9.68	4244	719	704	0.984	0.233	97.9
5.11-5.6	5.594	0.228	9	3435	673	614	0.965	0.253	91.2
5.6-6.26	6.776	0.201	11.4	4093	607	604	0.991	0.217	99.5
6.26-7.23	6.727	0.116	15.21	3626	537	539	0.997	0.125	100
7.23-8.85	6.738	0.062	24.02	3160	473	469	0.997	0.068	99.2
8.85-12.52	6.567	0.046	30.15	2443	372	372	0.999	0.05	100
12.52-44.421	5.692	0.041	30.56	1184	216	208	0.998	0.045	96.3

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.13_2998	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→44.421 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.01

	R_factor	Num. reflection	% reflection
R_free	0.2689	827	5 %
R_work	0.2183	-	-
obs	0.221	16533	98.63 %

Solvent computation

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

Displacement parameters

B_iso max: 133.46 Å² / B_iso mean: 54.9841 Å² / B_iso min: 11.59 Å²

Refinement step

Cycle: final / Resolution: 2.8→44.421 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4931	0	16	15	4962
B_iso mean	-	-	70.85	27.52	-
Num. residues	-	-	-	-	672

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.8002-2.9756	0.4348	134	0.3421	2531	97
2.9756-3.2053	0.3279	137	0.2954	2615	100
3.2053-3.5277	0.3359	138	0.2796	2608	100
3.5277-4.0379	0.2929	138	0.2113	2623	99
4.0379-5.0862	0.2411	138	0.1842	2626	99
5.0862-44.421	0.1847	142	0.1624	2703	98

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	2.8114	-2.1952	-2.6491	5.727	0.7777	3.4774	-1.4141	0.3771	-0.7985	0.9206	0.8494	-0.2776	1.0011	-0.458	0.4839	0.857	-0.0247	0.0396	0.6576	-0.0951	0.5379	40.0189	-17.5443	57.4593
2	9.48	-0.6515	0.2438	3.9929	-0.2669	3.8295	-0.2508	-0.31	-0.5481	0.0996	0.1791	-0.0168	0.0302	-0.5718	0.0785	0.5287	0.0745	-0.0649	0.4795	-0.018	0.4881	38.948	-10.4311	50.8244
3	4.6306	-0.607	-0.9686	3.4577	0.591	4.2451	0.2411	0.1617	0.3703	0.2826	0.1784	0.1883	-0.5144	-0.4935	-0.4178	0.388	0.0513	-0.0841	0.3254	0.1831	0.5906	40.5779	-2.4536	44.972
4	6.4775	-6.263	0.5941	6.0693	-0.5417	0.0868	-0.0025	0.3476	-0.4657	0.4789	-0.3884	0.7359	-0.0617	0.1738	0.4254	0.3915	-0.119	0.0349	0.3793	0.0265	0.4828	38.401	-8.3463	38.0122
5	3.0982	-0.3992	1.2762	1.4996	-0.4593	3.3386	-0.0682	-0.0508	-0.2466	0.1184	0.0132	-0.1181	0.0004	-0.1908	0.067	0.261	-0.017	-0.028	0.2883	0.0178	0.4574	36.7569	0.7243	28.2311
6	5.0538	-1.2421	-0.8837	2.0661	-1.0958	3.9548	-0.0617	0.36	0.2138	-0.1479	0.4275	-0.5202	-0.1913	0.2575	-0.4053	0.3308	-0.0061	0.018	0.2128	0.0338	0.3369	29.2153	6.3758	16.5088
7	4.3943	0.853	0.9437	8.9016	2.5257	5.2026	-0.1966	-0.3202	-0.434	0.0618	0.4575	0.3742	-0.1702	0.3812	-0.3105	0.3043	0.0524	0.0276	0.3508	0.1081	0.4939	22.1978	1.6957	20.8531
8	4.0523	0.4399	-1.1589	2.8604	-0.139	1.3257	0.0717	0.1132	0.355	-0.1855	0.015	0.2031	-0.0614	0.0737	-0.0544	0.2802	0.0162	-0.0897	0.3087	0.0265	0.4221	11.7682	9.3054	16.4773
9	9.7596	-6.3806	4.713	7.3741	-5.5131	6.8824	0.3961	-0.6937	0.3272	-1.2053	-0.0291	-0.4088	0.4161	-0.7465	-0.2924	0.4395	-0.1119	-0.0334	0.4044	-0.1188	0.2814	20.2223	8.9806	27.4591
10	6.5151	-2.5624	1.7418	4.2513	-0.9307	9.4492	-0.0693	-0.9086	0.7275	0.5601	0.4939	0.1594	-0.7189	0.8816	-0.6758	0.5196	0.0184	0.0192	0.5044	-0.1989	0.7022	13.3313	13.5188	50.9691
11	3.1232	1.7751	1.0166	1.9111	0.9466	1.7451	0.1073	-0.2252	0.1919	0.3613	-0.0127	-0.2147	0.0367	0.1572	-0.0665	0.3619	0.0536	-0.0269	0.2459	-0.0379	0.4374	3.5201	-1.5661	42.7216
12	0.9429	0.3575	0.2253	3.6614	0.3404	1.4132	0.1207	-0.1502	0.1137	0.0394	-0.2099	0.1611	0.046	-0.1599	0.2021	0.3163	-0.0406	-0.0489	0.371	-0.0858	0.4424	-9.2492	-13.9869	33.2869
13	4.077	-0.3303	-0.1818	2.5296	0.9221	2.9305	0.0548	0.1923	0.0778	-0.0709	-0.1586	-0.1021	0.0096	-0.2085	0.0319	0.2973	-0.073	-0.0202	0.2822	-0.0467	0.3581	-14.1861	-10.2415	20.6883
14	5.4942	0.0202	1.1219	4.8691	2.6579	6.1201	-0.0581	0.3101	-0.1528	-0.1534	0.199	-0.156	-0.2169	0.1888	-0.1619	0.4457	-0.0635	0.0259	0.3932	0.0095	0.2576	-13.3165	-8.1611	5.5399
15	2.7714	0.5338	0.8304	2.6226	0.7185	4.4116	0.1222	0.4028	0.0644	-0.6114	0.1817	-0.7104	-0.4355	0.3492	-0.0984	0.3384	-0.0896	-0.0022	0.3623	-0.0033	0.3427	-4.8434	-5.6519	10.888

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 5 through 33 )	A	5 - 33
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 74 )	A	34 - 74
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 75 through 101 )	A	75 - 101
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 102 through 117 )	A	102 - 117
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 118 through 201 )	A	118 - 201
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 202 through 227 )	A	202 - 227
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 228 through 243 )	A	228 - 243
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 244 through 325 )	A	244 - 325
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 326 through 344 )	A	326 - 344
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 4 through 32 )	B	4 - 32
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 33 through 159 )	B	33 - 159
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 160 through 185 )	B	160 - 185
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 186 through 269 )	B	186 - 269
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 270 through 311 )	B	270 - 311
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 312 through 344 )	B	312 - 344

-
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://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