PDB-6s9m: Designed Armadillo Repeat protein Lock2 fused to target peptide K...

ID or keywords:

Entry

Database: PDB / ID: 6s9m

Title

Designed Armadillo Repeat protein Lock2 fused to target peptide KRKRKAKITW

Components

Lock2_KRKRKAKITW

Keywords

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

Function / homology

Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha / TRIETHYLENE GLYCOL

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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	May 15, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6s9m.cif.gz	679.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6s9m.ent.gz	562.9 KB	Display	PDB format
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Validation report

Summary document	6s9m_validation.pdf.gz	497.6 KB	Display	wwPDB validaton report
Full document	6s9m_full_validation.pdf.gz	525.7 KB	Display
Data in XML	6s9m_validation.xml.gz	75.1 KB	Display
Data in CIF	6s9m_validation.cif.gz	108.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s9/6s9m ftp://data.pdbj.org/pub/pdb/validation_reports/s9/6s9m	HTTPS FTP

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Related structure data

Related structure data	6s9lC 6s9nC 6s9oC 6s9pC C: citing same article (ref.)
Similar structure data	6s9n-2 6s9n-5 6s9l-2 4l7m-1 5aei-2 6s9n-3 6s9n-4 5aei-3 5mfh-3 5aei-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

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	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Lock2_KRKRKAKITW

B: Lock2_KRKRKAKITW

C: Lock2_KRKRKAKITW

D: Lock2_KRKRKAKITW

E: Lock2_KRKRKAKITW

F: Lock2_KRKRKAKITW

hetero molecules

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

1

A: Lock2_KRKRKAKITW

hetero molecules

defined by author
Evidence: assay for oligomerization, fluorescence anisotropy binding experiments and stopped flow FRET kinetics
32 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Lock2_KRKRKAKITW

hetero molecules

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

3

C: Lock2_KRKRKAKITW

hetero molecules

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

4

D: Lock2_KRKRKAKITW

hetero molecules

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

5

E: Lock2_KRKRKAKITW

hetero molecules

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

6

F: Lock2_KRKRKAKITW

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.853, 85.474, 193.970
Angle α, β, γ (deg.)	90.000, 96.320, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	THR	THR	A	A	11 - 308	4 - 301
2	1	SER	SER	THR	THR	B	B	11 - 308	4 - 301
1	2	GLY	GLY	TRP	TRP	A	A	10 - 309	3 - 302
2	2	GLY	GLY	TRP	TRP	C	C	10 - 309	3 - 302
1	3	GLU	GLU	THR	THR	A	A	12 - 308	5 - 301
2	3	GLU	GLU	THR	THR	D	D	12 - 308	5 - 301
1	4	GLY	GLY	THR	THR	A	A	10 - 308	3 - 301
2	4	GLY	GLY	THR	THR	E	E	10 - 308	3 - 301
1	5	GLU	GLU	THR	THR	A	A	12 - 308	5 - 301
2	5	GLU	GLU	THR	THR	F	F	12 - 308	5 - 301
1	6	SER	SER	THR	THR	B	B	11 - 308	4 - 301
2	6	SER	SER	THR	THR	C	C	11 - 308	4 - 301
1	7	GLU	GLU	THR	THR	B	B	12 - 308	5 - 301
2	7	GLU	GLU	THR	THR	D	D	12 - 308	5 - 301
1	8	SER	SER	THR	THR	B	B	11 - 308	4 - 301
2	8	SER	SER	THR	THR	E	E	11 - 308	4 - 301
1	9	GLU	GLU	THR	THR	B	B	12 - 308	5 - 301
2	9	GLU	GLU	THR	THR	F	F	12 - 308	5 - 301
1	10	GLU	GLU	THR	THR	C	C	12 - 308	5 - 301
2	10	GLU	GLU	THR	THR	D	D	12 - 308	5 - 301
1	11	GLY	GLY	THR	THR	C	C	10 - 308	3 - 301
2	11	GLY	GLY	THR	THR	E	E	10 - 308	3 - 301
1	12	GLU	GLU	THR	THR	C	C	12 - 308	5 - 301
2	12	GLU	GLU	THR	THR	F	F	12 - 308	5 - 301
1	13	GLU	GLU	THR	THR	D	D	12 - 308	5 - 301
2	13	GLU	GLU	THR	THR	E	E	12 - 308	5 - 301
1	14	GLU	GLU	TRP	TRP	D	D	12 - 309	5 - 302
2	14	GLU	GLU	TRP	TRP	F	F	12 - 309	5 - 302
1	15	GLU	GLU	THR	THR	E	E	12 - 308	5 - 301
2	15	GLU	GLU	THR	THR	F	F	12 - 308	5 - 301

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Lock2_KRKRKAKITW Mass: 31502.402 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 1109 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1072 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.88 %
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

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 1.000041 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2017

Radiation

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

Radiation wavelength

Wavelength: 1.000041 Å / Relative weight: 1

Reflection

Resolution: 2→48.2 Å / Num. obs: 228033 / % possible obs: 96.3 % / Redundancy: 3.479 % / B_iso Wilson estimate: 34.082 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.112 / R_rim(I) all: 0.133 / Χ²: 1.017 / Net I/σ(I): 10.55 / Num. measured all: 793257 / Scaling rejects: 60

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
2-2.05	3.423	0.871	1.72	57781	17587	16882	0.626	1.038	96
2.05-2.11	3.302	0.713	2.04	53572	17163	16224	0.7	0.854	94.5
2.11-2.17	2.998	0.516	2.61	44230	16463	14753	0.815	0.63	89.6
2.17-2.24	3.378	0.446	3.39	51676	16155	15300	0.873	0.534	94.7
2.24-2.31	3.533	0.387	4.09	53505	15726	15146	0.899	0.46	96.3
2.31-2.39	3.524	0.305	5.36	51205	15057	14531	0.922	0.363	96.5
2.39-2.48	3.533	0.273	6.56	49964	14607	14141	0.933	0.325	96.8
2.48-2.58	3.511	0.25	7.29	47604	14027	13559	0.938	0.299	96.7
2.58-2.7	3.579	0.237	8.4	46711	13376	13051	0.946	0.281	97.6
2.7-2.83	3.669	0.231	9.83	46710	12866	12732	0.957	0.272	99
2.83-2.98	3.639	0.182	11.76	44183	12276	12141	0.972	0.214	98.9
2.98-3.16	3.592	0.148	13.38	41081	11585	11436	0.98	0.175	98.7
3.16-3.38	3.532	0.113	15.63	37535	10847	10626	0.988	0.135	98
3.38-3.65	3.459	0.085	18.68	33884	10150	9797	0.993	0.1	96.5
3.65-4	3.119	0.055	22.21	26648	9240	8543	0.996	0.066	92.5
4-4.47	3.407	0.043	26.43	27641	8440	8114	0.997	0.051	96.1
4.47-5.16	3.765	0.043	27.89	27898	7431	7410	0.998	0.05	99.7
5.16-6.32	3.797	0.046	26.07	23647	6250	6227	0.998	0.054	99.6
6.32-8.94	3.781	0.031	33.69	18257	4839	4829	0.999	0.037	99.8
8.94-48.2	3.676	0.024	40.68	9525	2647	2591	0.999	0.028	97.9

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC	5.8.0189	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→48.2 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.945 / SU B: 8.503 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.157
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2126	5904	5 %	RANDOM
R_work	0.177	-	-	-
obs	0.1788	112173	98.04 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 167.65 Å² / B_iso mean: 32.384 Å² / B_iso min: 12.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.3 Å²	-0 Å²	-1.03 Å²
2-	-	0.08 Å²	0 Å²
3-	-	-	-2.1 Å²

Refinement step

Cycle: final / Resolution: 2→48.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13207	0	139	1072	14418
B_iso mean	-	-	64.03	40.04	-
Num. residues	-	-	-	-	1796

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.019	13700
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	12969
X-RAY DIFFRACTION	r_angle_refined_deg	1.948	1.982	18574
X-RAY DIFFRACTION	r_angle_other_deg	1.079	3	30405
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.293	5	1841
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.382	28.462	598
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.752	15	2415
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.16	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	2172
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	15586
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2067

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	18640	0.07
1	2	B	18640	0.07
2	1	A	18612	0.09
2	2	C	18612	0.09
3	1	A	18470	0.08
3	2	D	18470	0.08
4	1	A	18516	0.08
4	2	E	18516	0.08
5	1	A	18272	0.09
5	2	F	18272	0.09
6	1	B	18514	0.09
6	2	C	18514	0.09
7	1	B	18544	0.08
7	2	D	18544	0.08
8	1	B	18492	0.08
8	2	E	18492	0.08
9	1	B	18402	0.09
9	2	F	18402	0.09
10	1	C	18250	0.09
10	2	D	18250	0.09
11	1	C	18356	0.09
11	2	E	18356	0.09
12	1	C	18144	0.1
12	2	F	18144	0.1
13	1	D	18592	0.08
13	2	E	18592	0.08
14	1	D	18682	0.09
14	2	F	18682	0.09
15	1	E	18454	0.08
15	2	F	18454	0.08

LS refinement shell

Resolution: 2→2.052 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	433	-
R_work	0.287	8224	-
all	-	8657	-
obs	-	-	97.5 %

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	0.0728	-0.1476	-0.0519	0.3186	0.063	0.2984	0.0112	0.0065	-0.0064	-0.0308	-0.048	0.0175	0.0351	0.0132	0.0368	0.0211	0.0035	0.0381	0.0774	-0.0064	0.1045	1.992	23.8223	47.723
2	0.0565	-0.1339	-0.0282	0.3791	0.2178	0.562	-0.013	0.0173	-0.0173	-0.009	-0.0556	0.0359	-0.0428	0.0225	0.0686	0.047	0.0101	0.0239	0.0398	0.0012	0.1024	24.667	-20.0136	15.9906
3	0.2271	-0.1517	0.0167	0.1134	0.1625	2.5782	0.022	0.0549	0.1128	0.0139	-0.059	-0.0739	0.3598	-0.3921	0.0369	0.0733	-0.0711	0.0143	0.1137	0.0176	0.0572	11.6995	-15.7734	-12.8494
4	0.1315	0.1744	0.1731	0.3296	-0.0069	0.8055	-0.0185	-0.0196	0.0299	-0.0378	-0.0467	0.0159	0.0073	0.0113	0.0653	0.0173	-0.008	0.0318	0.0697	0.0037	0.122	29.7685	-28.5703	52.0062
5	0.0141	0.0413	-0.0572	0.2364	0.1007	0.8812	-0.0032	-0.0039	-0.0071	0.0185	-0.0306	-0.039	0.0824	-0.0337	0.0338	0.0168	-0.0193	0.0183	0.0651	0.0215	0.1058	8.2197	14.9391	77.9339
6	0.4182	-0.0516	0.3803	0.2979	0.0876	0.5492	-0.074	0.0116	0.0603	-0.0135	-0.0161	-0.003	0.0049	0.0079	0.0901	0.0572	0.0049	0.0164	0.0825	0.0077	0.0989	5.0986	8.0796	109.2078

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 309
2	X-RAY DIFFRACTION	2	B	11 - 309
3	X-RAY DIFFRACTION	3	C	10 - 309
4	X-RAY DIFFRACTION	4	D	12 - 309
5	X-RAY DIFFRACTION	5	E	9 - 309
6	X-RAY DIFFRACTION	6	F	12 - 309

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 5 types, 1109 molecules

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-Protein , 1 types, 6 molecules ABCDEF

-Non-polymers , 5 types, 1109 molecules

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+About Yorodumi

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 5 types, 1109 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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

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Yorodumi