PDB-4j7w: E3_5 DARPin L86A mutant

ID or keywords:

Entry

Database: PDB / ID: 4j7w

Title

E3_5 DARPin L86A mutant

Components

DARPin_E3_5_L86A

Keywords

DE NOVO PROTEIN / Protein Design / DARPins / ankyrin repeat protein / unselected DARPin

Function / homology

Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Seeger, M.A. / Gruetter, M.G.

Citation

Journal: Protein Sci. / Year: 2013
Title: Design, construction, and characterization of a second-generation DARPin library with reduced hydrophobicity.
Authors: Seeger, M.A. / Zbinden, R. / Flutsch, A. / Gutte, P.G. / Engeler, S. / Roschitzki-Voser, H. / Grutter, M.G.

History

Deposition	Feb 14, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Feb 28, 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

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PDBx/mmCIF format	4j7w.cif.gz	131.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4j7w.ent.gz	103.4 KB	Display	PDB format
PDBx/mmJSON format	4j7w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4j7w_validation.pdf.gz	419.4 KB	Display	wwPDB validaton report
Full document	4j7w_full_validation.pdf.gz	420.5 KB	Display
Data in XML	4j7w_validation.xml.gz	17.6 KB	Display
Data in CIF	4j7w_validation.cif.gz	27.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j7/4j7w ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j7w	HTTPS FTP

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Related structure data

Related structure data	4j8yC 4jb8C 1mj0 C: citing same article (ref.)
Similar structure data	1mx4-2 4zfh-d 5kng-1 6fpb-d 5kng-2 4gpm-2 2xee-3 5lw2-d 4j8y-d 4hll-d 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

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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: DARPin_E3_5_L86A

B: DARPin_E3_5_L86A

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

1

A: DARPin_E3_5_L86A

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

2

B: DARPin_E3_5_L86A

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

Unit cell

Length a, b, c (Å)	44.370, 78.590, 82.230
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DARPin_E3_5_L86A Mass: 18053.025 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 455 / 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: 1.99 Å³/Da / Density % sol: 38.05 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Na-Citrate, 20% 2-propanol, 20% PEG4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2011
Radiation	Monochromator: X06DA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. all: 38712 / Num. obs: 38289 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 %
Reflection shell	Resolution: 1.6→1.64 Å / % possible all: 99.4

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Processing

Software

Name	Version	Classification
XDS		data scaling
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→41.115 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 17.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1862	1911	5 %	randomly chonsen by phenix
R_work	0.1615	-	-	-
obs	0.1627	38225	98.74 %	-
all	-	38712	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.6→41.115 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2342	0	0	455	2797

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2437
X-RAY DIFFRACTION	f_angle_d	1.021	3328
X-RAY DIFFRACTION	f_dihedral_angle_d	12.953	886
X-RAY DIFFRACTION	f_chiral_restr	0.07	394
X-RAY DIFFRACTION	f_plane_restr	0.005	447

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 (%)
1.6-1.64	0.202	136	0.1451	2585	X-RAY DIFFRACTION	100
1.64-1.6844	0.1914	134	0.1513	2543	X-RAY DIFFRACTION	100
1.6844-1.7339	0.2103	136	0.1494	2594	X-RAY DIFFRACTION	100
1.7339-1.7899	0.2129	136	0.1652	2587	X-RAY DIFFRACTION	100
1.7899-1.8539	0.2392	137	0.1638	2593	X-RAY DIFFRACTION	100
1.8539-1.9281	0.2687	130	0.2143	2486	X-RAY DIFFRACTION	95
1.9281-2.0158	0.1925	135	0.1706	2560	X-RAY DIFFRACTION	99
2.0158-2.1221	0.1916	137	0.1527	2605	X-RAY DIFFRACTION	100
2.1221-2.2551	0.1612	131	0.1742	2481	X-RAY DIFFRACTION	96
2.2551-2.4292	0.221	134	0.1608	2560	X-RAY DIFFRACTION	97
2.4292-2.6736	0.1748	138	0.1612	2620	X-RAY DIFFRACTION	100
2.6736-3.0603	0.1721	140	0.1637	2651	X-RAY DIFFRACTION	100
3.0603-3.8553	0.1664	139	0.1486	2645	X-RAY DIFFRACTION	99
3.8553-41.115	0.1561	148	0.157	2804	X-RAY DIFFRACTION	99

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	0.003	0.0023	0.0023	0.0017	0.0017	0.0017	0.0023	-0.0009	0.0121	-0.0028	-0.0122	0.0001	0.0059	0.0021	-0.0058	-0.0064	0.0117	0.0105	0.0231	0.0038	0.0214	6.3078	18.5259	-5.7429
2	0.0093	-0.0094	0.0219	0.0111	-0.0186	0.0599	0.0112	0.0039	-0.0242	-0.0093	0.0189	0.0151	0.0149	-0.0109	0.0428	-0.0283	0.0196	-0.0246	0.0008	0.0128	0.0204	6.8949	14.809	4.2013
3	0.0018	-0.0016	0.0001	0.0013	-0.0005	0.0021	0.0008	-0.001	-0.0034	0.0011	0	0.008	-0.0029	-0.003	0.0034	0.0014	0.0012	0.0158	-0.0033	-0.0079	0.0195	3.9052	20.4187	15.3021
4	-0	-0.0008	0.0008	0.0076	-0.007	0.0066	0.009	-0.0021	-0.0136	0.0003	0.0088	0.0104	0.0094	-0.0023	0.0153	0.0322	0.0278	-0.0164	0.0232	0.011	0.0147	16.292	11.0802	18.5077
5	0.009	0.0014	-0.0126	0.0002	-0.0019	0.0186	0.0035	-0.0073	0.0015	0.0192	0.0066	0.0055	-0.0072	0.0025	0.0121	0.0388	0.0186	0.0218	0.0228	-0.0018	-0.001	13.2069	20.6209	22.8597
6	0.0159	-0.0089	-0.0013	0.0051	0.0008	0.0002	-0.002	0.0013	0.003	0.001	-0.0035	-0.007	0.0011	0.002	-0.0034	0.049	0.031	-0.0179	0.0717	0.0077	0.0571	23.9973	10.1554	24.4653
7	0.001	0.0001	0.0003	0.0012	-0	0.0005	0.0159	0.0004	0.0096	0.0083	0.0027	-0.0045	-0.0082	-0.0005	0.0021	0.0812	-0.0113	0.027	0.0769	-0.0056	0.0766	23.8564	23.1124	26.7967
8	0.0019	0.0005	0.0025	0.0003	0.0004	0.0044	0.0054	-0.001	-0.0024	0.0028	0.0037	0.0012	0.0023	0.0019	0.0015	0.0821	-0.0029	-0.0081	0.0929	0.0061	0.045	18.1234	18.5461	34.3234
9	0.0011	-0.0007	-0.0011	0.0013	0	0.002	0.0151	0.0245	-0.0029	-0.0099	-0.0063	-0.0187	-0.0032	0.0075	0	0.0492	-0.0036	0.0102	0.0268	0.0095	0.0386	9.7064	39.3085	6.1583
10	0.0336	0.0086	-0.0171	0.0402	-0.0142	0.0122	0.0014	-0.0045	0.0292	0.0013	-0.0005	-0.0046	0.0321	-0.0407	0.0246	0.0322	-0.039	0.003	0.0166	-0.0139	0.0136	2.6304	38.2512	16.9775
11	0.0085	-0.0023	0.001	0.0014	0.0011	0.003	0.0048	-0.0025	0.0091	0.0041	0.0047	-0.0016	-0.0045	0.0066	0.0131	0.0214	-0.0056	0.0205	0.0238	-0.0226	0.0552	5.4258	43.4328	26.9814
12	0.0047	-0.0022	-0.0004	0.0069	-0.004	0.0028	-0.0182	-0.0053	-0.0116	0.009	0.0006	0.0066	0.0303	-0.0208	-0.0111	0.0983	-0.0291	0.0257	0.0681	-0.0123	0.0321	-2.2645	30.8928	30.5764
13	0.0009	-0.0001	-0.0002	0.0012	0.0005	0.0002	-0.0022	0.0032	0.0085	0.0089	-0.0029	-0.0056	-0.0024	0.0078	-0	0.0711	0.004	0.0019	0.0337	-0.0069	0.0389	4.8522	39.1502	36.5043
14	0.0105	0.0053	-0.0149	0.0052	-0.0111	0.0261	0.0157	-0.0087	0.0073	0.0005	0.0079	-0.0012	0.0096	-0.0089	0.0081	0.0963	-0.0655	0.0122	0.1175	-0.0096	0.0707	-8.9573	29.8082	35.8216
15	0.002	-0.0024	0.0013	0.003	-0.0017	0.0009	-0.0029	-0.0023	-0.0091	-0.0016	-0.0066	-0.0094	0.0084	-0.0004	-0.003	0.1022	-0.0249	0.0211	0.0386	0.0038	0.0435	-0.9563	23.3435	38.4796
16	0.0007	-0.0006	0.0003	0.0015	0.0001	0.0012	-0.0072	-0.0007	-0.0054	0.0006	-0.0059	0.0003	0.0001	-0.0027	-0	0.0966	-0.0081	-0.0125	0.1297	0.01	0.0671	2.6412	28.7225	46.1514

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 13:29)
2	X-RAY DIFFRACTION	2	(chain A and resid 30:91)
3	X-RAY DIFFRACTION	3	(chain A and resid 92:103)
4	X-RAY DIFFRACTION	4	(chain A and resid 104:119)
5	X-RAY DIFFRACTION	5	(chain A and resid 120:139)
6	X-RAY DIFFRACTION	6	(chain A and resid 140:149)
7	X-RAY DIFFRACTION	7	(chain A and resid 150:164)
8	X-RAY DIFFRACTION	8	(chain A and resid 165:169)
9	X-RAY DIFFRACTION	9	(chain B and resid 13:36)
10	X-RAY DIFFRACTION	10	(chain B and resid 37:92)
11	X-RAY DIFFRACTION	11	(chain B and resid 93:105)
12	X-RAY DIFFRACTION	12	(chain B and resid 106:126)
13	X-RAY DIFFRACTION	13	(chain B and resid 127:135)
14	X-RAY DIFFRACTION	14	(chain B and resid 136:147)
15	X-RAY DIFFRACTION	15	(chain B and resid 148:158)
16	X-RAY DIFFRACTION	16	(chain B and resid 159:169)

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