PDB-5cwl: Crystal structure of de novo designed helical repeat protein DHR54

ID or keywords:

Entry

Database: PDB / ID: 5cwl

Title

Crystal structure of de novo designed helical repeat protein DHR54

Components

Designed helical repeat protein

Keywords

DE NOVO PROTEIN / helical repeat protein

Function / homology

TRIETHYLENE GLYCOL

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.5 Å

Authors

Bhabha, G. / Ekiert, D.C.

Citation

Journal: Nature / Year: 2015
Title: Exploring the repeat protein universe through computational protein design.
Authors: Brunette, T.J. / Parmeggiani, F. / Huang, P.S. / Bhabha, G. / Ekiert, D.C. / Tsutakawa, S.E. / Hura, G.L. / Tainer, J.A. / Baker, D.

History

Deposition	Jul 28, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2015	Group: Database references
Revision 1.2	Jan 6, 2016	Group: Database references
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cwl.cif.gz	227.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5cwl.ent.gz	189.2 KB	Display	PDB format
PDBx/mmJSON format	5cwl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5cwl_validation.pdf.gz	446.7 KB	Display	wwPDB validaton report
Full document	5cwl_full_validation.pdf.gz	447.8 KB	Display
Data in XML	5cwl_validation.xml.gz	15.8 KB	Display
Data in CIF	5cwl_validation.cif.gz	22.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cw/5cwl ftp://data.pdbj.org/pub/pdb/validation_reports/cw/5cwl	HTTPS FTP

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Related structure data

Related structure data	5cwbC 5cwcC 5cwdC 5cwfC 5cwgC 5cwhC 5cwiC 5cwjC 5cwkC 5cwmC 5cwnC 5cwoC 5cwpC 5cwqC C: citing same article (ref.)
Similar structure data	6n6d-d 2v0v-3 4nto-3 2f4i-3 6l9k-d 4nto-1 4nto-2 2f4i-2 4nt2-d 4lrk-2 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: Designed helical repeat protein

B: Designed helical repeat protein

hetero molecules

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

1

A: Designed helical repeat protein

hetero molecules

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

2

B: Designed helical repeat protein

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

Unit cell

Length a, b, c (Å)	55.250, 69.100, 82.630
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Designed helical repeat protein Mass: 20301.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.94 Å³/Da / Density % sol: 36.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M Sodium chloride, 0.1 M Na/K phosphate, pH 6.2, 50% (v/v) PEG 200

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.111 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2015

Radiation

Monochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.111 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 51178 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7 % / B_iso Wilson estimate: 23.18 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.056 / R_rim(I) all: 0.061 / Χ²: 0.991 / Net I/σ(I): 15.08 / Num. measured all: 360741

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.5-1.54		7.1	0.489	1.802	1.03	26354	3723	3720	1.946	99.9
1.54-1.58			0.497	1.659	1.16	25799	3642	3640	1.792	99.9
1.58-1.63			0.58	1.329	1.48	25456	3586	3584	1.436	99.9
1.63-1.68			0.752	1.018	1.95	24596	3454	3452	1.099	99.9
1.68-1.73			0.809	0.807	2.45	23938	3358	3356	0.871	99.9
1.73-1.79			0.879	0.588	3.41	23224	3243	3241	0.635	99.9
1.79-1.86			0.958	0.403	4.93	22467	3131	3129	0.434	99.9
1.86-1.94			0.971	0.282	7.02	21608	3012	3010	0.305	99.9
1.94-2.02			0.986	0.186	10.36	20931	2910	2908	0.2	99.9
2.02-2.12			0.994	0.114	15.61	20154	2814	2811	0.123	99.9
2.12-2.24			0.997	0.084	20.35	18855	2633	2631	0.091	99.9
2.24-2.37			0.998	0.065	25.59	17994	2523	2521	0.07	99.9
2.37-2.54			0.998	0.054	29.21	16770	2369	2367	0.059	99.9
2.54-2.74			0.998	0.049	33.14	15399	2203	2195	0.052	99.6
2.74-3			0.999	0.042	37.13	14056	2056	2044	0.045	99.4
3-3.35			0.999	0.038	39.85	12548	1872	1864	0.041	99.6
3.35-3.87			0.999	0.034	44.81	11171	1650	1643	0.036	99.6
3.87-4.74			0.999	0.032	46.76	9336	1421	1408	0.035	99.1
4.74-6.71			0.999	0.032	45.03	7307	1132	1122	0.035	99.1
	6.71		0.998	0.031	40.53	2778	675	532	0.035	78.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building
PHENIX	(phenix.refine: 1.9_1692)	refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→45.929 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2091	1817	3.88 %	RANDOM
R_work	0.1793	45067	-	-
obs	0.1805	46884	91.32 %	-

Solvent computation

Shrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 210.29 Å² / B_iso mean: 47.768 Å² / B_iso min: 18.79 Å²

Refinement step

Cycle: final / Resolution: 1.5→45.929 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2703	0	55	162	2920
B_iso mean	-	-	72.65	49.43	-
Num. residues	-	-	-	-	352

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3019
X-RAY DIFFRACTION	f_angle_d	0.698	4086
X-RAY DIFFRACTION	f_chiral_restr	0.028	468
X-RAY DIFFRACTION	f_plane_restr	0.002	566
X-RAY DIFFRACTION	f_dihedral_angle_d	12.601	1224

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5-1.5406	0.4569	113	0.3588	2828	2941	76
1.5406-1.5859	0.3698	114	0.333	2944	3058	78
1.5859-1.6371	0.3096	123	0.2961	3095	3218	82
1.6371-1.6956	0.3104	121	0.2686	3185	3306	85
1.6956-1.7635	0.3153	137	0.2481	3297	3434	88
1.7635-1.8438	0.2293	143	0.2167	3430	3573	91
1.8438-1.941	0.1979	137	0.2014	3533	3670	94
1.941-2.0626	0.2188	154	0.1775	3703	3857	98
2.0626-2.2219	0.1831	153	0.1565	3756	3909	99
2.2219-2.4455	0.1652	153	0.149	3775	3928	100
2.4455-2.7993	0.1935	154	0.1573	3799	3953	99
2.7993-3.5266	0.1847	158	0.1712	3850	4008	100
3.5266-45.9504	0.2144	157	0.1714	3872	4029	96

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	0.2913	-0.0099	-0.0512	0.2039	0.0824	0.0909	0.0867	0.0725	0.0539	-0.2591	0.5686	0.7542	0.045	-0.9378	-0.0005	0.3537	-0.028	-0.0505	0.6089	0.0814	0.5007	-16.6002	12.7061	-21.7028
2	0.5856	-0.1022	0.6456	2.0188	-0.3515	1.1062	0.0559	0.0704	-0.0464	-0.2064	-0.0854	-0.1089	0.0439	-0.0558	0	0.2235	0.0261	0.0107	0.2333	0.0058	0.2263	-7.3369	18.4977	-15.159
3	0.6194	-0.5821	0.5415	1.8192	0.5783	1.5176	0.0653	0.0106	0.0139	0.0432	-0.1106	-0.2986	-0.0357	0.104	0	0.1945	-0.0056	-0.0003	0.2311	0.0226	0.2248	-1.3564	27.6251	-4.6919
4	0.6085	-0.8802	-0.2732	1.573	-0.0972	1.0182	0.1506	0.2796	0.2559	0.105	-0.3253	-1.1471	-0.1365	0.9617	-0.0315	0.344	-0.0658	-0.0586	0.5053	0.0819	0.4933	6.6533	30.7538	-1.7293
5	0.0777	-0.1506	-0.003	0.4743	0.4124	2.2173	-0.1253	0.504	0.2461	-0.4639	0.0312	0.4182	0.1436	-0.8787	-0.4596	0.397	0.0104	-0.1436	0.5799	0.1372	0.3214	-36.0557	26.642	-22.127
6	1.3007	0.2179	0.3854	0.65	-0.8348	1.7346	0.0794	0.5636	-0.1467	-1.22	0.0848	-0.5132	0.3781	-0.1876	0.77	0.6252	0.0871	0.1862	0.4528	0.0389	0.3489	-25.9751	25.3873	-21.278
7	0.3398	-0.321	-0.1105	0.8921	0.565	0.3663	0.1107	0.365	0.2378	-0.3177	0.3873	0.3229	-0.4184	-0.864	0.0093	0.3241	0.059	0.0335	0.353	0.0992	0.2446	-32.5593	32.9566	-14.9317
8	0.6825	-0.348	-0.0092	1.6481	0.6533	1.8291	0.0488	0.1106	0.1681	-0.2799	0.0077	-0.4267	-0.281	0.2742	0.0003	0.2603	0.0111	0.0604	0.2659	0.0436	0.3061	-23.0276	33.8618	-7.885
9	0.668	-0.2212	0.3136	0.4676	0.3348	0.5693	0.1563	0.1299	0.1752	0.1309	0.0081	0.0558	-0.7253	-0.189	0.0001	0.4015	0.0192	0.0459	0.233	0.0203	0.3078	-25.6568	43.1355	0.6632
10	0.3943	0.4333	-0.0049	0.8567	0.3119	0.2752	-0.2043	-0.2178	0.1018	0.1801	-0.0411	-0.6672	-0.1218	0.4974	-0.0119	0.2769	-0.0574	-0.0088	0.3582	0.0283	0.4536	-15.5039	39.4219	3.826

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 2:22 )	A	2 - 22
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 23:109 )	A	23 - 109
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 110:154 )	A	110 - 154
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 155:178 )	A	155 - 178
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 2:23 )	B	2 - 23
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 24:45 )	B	24 - 45
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 46:66 )	B	46 - 66
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 67:131 )	B	67 - 131
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 132:154 )	B	132 - 154
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 155:176 )	B	155 - 176

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