PDB-5dqa: t3284 loop variant of beta1

ID or keywords:

Entry

Database: PDB / ID: 5dqa

Title

t3284 loop variant of beta1

Components

t3284

Keywords

DE NOVO PROTEIN / synthetic protein / loop design

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.27 Å

Authors

Kabasakal, B.V. / MacDonald, J.T. / Murray, W.W.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.
Authors: MacDonald, J.T. / Kabasakal, B.V. / Godding, D. / Kraatz, S. / Henderson, L. / Barber, J. / Freemont, P.S. / Murray, J.W.

History

Deposition	Sep 14, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 31, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2016	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	5dqa.cif.gz	250.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5dqa_validation.pdf.gz	442.1 KB	Display	wwPDB validaton report
Full document	5dqa_full_validation.pdf.gz	443.3 KB	Display
Data in XML	5dqa_validation.xml.gz	21.9 KB	Display
Data in CIF	5dqa_validation.cif.gz	30.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/5dqa ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqa	HTTPS FTP

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Related structure data

Related structure data	4yc5C 4ycqC 4ydtC 4yeiC 4yfoC 5di5C 5dn0C 5dnsC 5draC 5dzbC C: citing same article (ref.)
Similar structure data	4yc5-1 4ydt-2 4ydt-1 4x0j-2 4mkm-d 3shs-d 5dn0-1 1qbp-d 3vp8-d 5n40-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) Search similar-shape structures by Omokage search (details)

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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: t3284

B: t3284

C: t3284

76.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: t3284

B: t3284

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

2

A: t3284

defined by author&software
51 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: t3284

C: t3284

defined by author&software
51 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.060, 115.710, 167.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	B
2	3	C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 21 - 241 / Label seq-ID: 21 - 241

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	B	B
2	3	C	C

NCS ensembles :

ID
1
2
3

#1: Protein	t3284 Mass: 25501.869 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pRSETA / Production host: Escherichia coli (E. coli)

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.37 Å³/Da / Density % sol: 63.46 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1M MES pH 6.5, 1.6 M magnesium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 3.27→53.03 Å / Num. all: 108277 / Num. obs: 16280 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / R_merge(I) obs: 0.062 / Net I/σ(I): 19
Reflection shell	Resolution: 3.27→3.35 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.67 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0131	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.27→53.03 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.958 / SU B: 47.301 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21073	807	5 %	RANDOM
R_work	0.1833	-	-	-
obs	0.18468	15473	99.57 %	-

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: 118.17 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	10.67 Å²	0 Å²	0 Å²
2-	-	-8.52 Å²	0 Å²
3-	-	-	-2.15 Å²

Refinement step

Cycle: 1 / Resolution: 3.27→53.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4709	0	0	0	4709

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	4750
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	4538
X-RAY DIFFRACTION	r_angle_refined_deg	1.972	1.944	6450
X-RAY DIFFRACTION	r_angle_other_deg	1.376	3	10284
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.218	5	641
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.025	25.366	246
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.615	15	717
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.613	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	755
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	5809
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1140
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.268	3.565	2582
X-RAY DIFFRACTION	r_mcbond_other	2.266	3.564	2581
X-RAY DIFFRACTION	r_mcangle_it	3.787	5.335	3217
X-RAY DIFFRACTION	r_mcangle_other	3.787	5.336	3218
X-RAY DIFFRACTION	r_scbond_it	3.054	4.068	2168
X-RAY DIFFRACTION	r_scbond_other	3.054	4.069	2169
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.954	5.92	3234
X-RAY DIFFRACTION	r_long_range_B_refined	9.248	34.785	21038
X-RAY DIFFRACTION	r_long_range_B_other	9.249	34.783	21037
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	26060	0.04
1	2	B	26060	0.04
2	1	A	25990	0.04
2	2	C	25990	0.04
3	1	B	26134	0.02
3	2	C	26134	0.02

LS refinement shell

Resolution: 3.27→3.355 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	65	-
R_work	0.312	1111	-
obs	-	-	99.92 %

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	21.8199	41.0416	10.8492	78.3398	20.9167	5.6503	-3.3694	1.7872	2.0023	-4.0154	2.7587	3.5783	-0.6268	0.8714	0.6107	5.2679	-0.3662	-0.509	2.8484	-0.9915	2.461	-1.294	-42.763	-38.002
2	5.2642	3.5409	-1.4118	12.3923	4.146	15.8992	-0.5721	1.456	-1.36	-1.2172	0.0951	-0.355	1.9053	0.0048	0.477	1.0948	-0.0751	0.3844	1.1743	-1.0456	1.0261	-4.737	-36.918	-34.899
3	0.8158	-2.4243	-0.8201	13.712	0.1671	13.1786	-0.3125	0.1638	0.2138	-1.7758	-0.3451	-0.6046	1.3991	-0.0205	0.6576	1.2677	-0.1521	0.0128	1.1435	-0.5814	0.7217	-3.559	-28.021	-32.309
4	9.4685	-2.5921	-0.1347	9.4678	-0.5165	9.159	-0.2838	0.9756	-0.8472	-0.4679	-0.2446	-0.1263	0.6119	-0.0476	0.5285	0.7819	-0.1048	0.3002	0.9266	-0.6673	0.6428	-6.011	-25.789	-22.908
5	0.9991	-1.5849	-1.6189	7.5195	3.5842	7.3302	0.0177	0.6819	-0.5192	-0.3226	-0.6478	0.1285	0.7061	-0.4339	0.6302	0.5605	-0.117	0.138	0.8629	-0.3383	0.516	-7.243	-19.349	-14.387
6	7.8437	-4.3197	-0.0552	12.9376	2.7814	8.4656	-0.5173	0.6518	-0.3387	-1.1085	-0.2841	-0.7919	0.0418	-0.0792	0.8014	0.5948	-0.0836	0.1884	0.6629	-0.1766	0.2773	-3.721	-11.39	-15.495
7	10.8456	-2.8948	1.1192	10.5576	0.6346	5.0678	0.1738	1.051	-0.858	-0.7453	-0.5388	0.2327	0.3047	0.1873	0.3649	0.5441	-0.0459	0.1452	0.7945	-0.293	0.2425	-7.252	-12.459	-10.119
8	3.8417	-3.7437	-1.1539	9.0768	6.1064	4.9349	-0.3675	-0.0153	-0.0365	0.2282	-0.2209	0.5153	-0.0678	-0.3513	0.5885	0.5695	-0.0299	0.0304	0.891	-0.3466	0.5925	-11.35	-10.5	-5.017
9	4.3634	2.787	-5.7862	3.1112	-3.49	7.7163	-0.0321	0.1562	-0.4576	0.1287	-0.6753	0.609	-0.0834	-0.2646	0.7074	0.648	-0.0452	0.0288	0.8482	-0.3171	0.7324	-6.494	-4.568	-7.779
10	5.8986	-0.8735	0.848	2.128	2.2945	3.5511	-0.1374	-0.037	-0.0906	0.1912	-0.6885	0.6871	0.1212	-0.5592	0.826	0.4548	-0.026	0.0872	0.8349	-0.1866	0.3786	-13.381	-3.26	1.133
11	25.3693	22.3285	11.4884	23.1076	9.7986	5.2368	-0.4971	1.2392	-1.2158	-1.1894	1.0333	-0.4203	-0.1803	0.5022	-0.5362	0.8845	-0.0303	-0.4881	0.853	-0.7966	1.0583	-42.516	-36.36	-45.421
12	7.9182	1.8071	1.9355	8.0471	0.8674	13.447	-0.1773	1.9488	-1.7674	-0.4614	0.0034	-0.153	1.0137	-0.3348	0.1739	1.2157	-0.0991	-0.2627	1.2633	-1.1739	1.2096	-37.424	-30.312	-42.715
13	15.2257	-2.0843	-1.2818	15.0388	-4.0011	14.866	0.4657	1.4511	-1.7454	-1.7231	-0.1536	0.8283	1.301	-0.4382	-0.3121	0.9105	-0.1056	-0.2779	0.8504	-0.7806	0.8789	-37.637	-25.815	-39.166
14	1.9165	1.505	-2.6139	15.3667	-2.5643	13.0412	0.2707	0.7207	-0.7405	-0.251	-0.2268	0.3311	0.668	-0.5662	-0.0439	0.8419	0.0033	-0.426	0.9142	-0.7782	0.8792	-36.247	-22.698	-36.018
15	6.9289	3.7833	5.2765	10.1311	1.4644	11.6158	0.0064	0.7692	-0.8263	-0.9459	-0.0654	-0.2405	1.0784	-0.3311	0.059	0.81	0.0054	-0.1744	0.9689	-0.7427	0.8325	-33.187	-18.913	-32.148
16	23.2988	2.5306	-8.1898	3.0207	4.6607	24.2219	0.2905	1.4379	0.4214	-0.7358	0.3591	0.4781	-0.8362	-1.5206	-0.6497	0.7666	-0.1289	-0.3612	0.9687	-0.26	1.0209	-39.156	-12.561	-30.415
17	6.4389	1.8475	1.3263	9.1418	1.1118	8.2541	0.493	0.5171	-0.8104	-0.2813	-0.5564	-0.197	0.2259	-0.3177	0.0635	0.6812	0.0615	-0.3089	0.8112	-0.4937	0.6516	-33.766	-12.519	-26.171
18	2.8377	-5.0283	-3.0607	10.5768	7.2609	9.4943	0.5995	0.4033	-0.4726	-0.2446	-0.5701	0.1672	-0.2276	-0.4448	-0.0293	0.6411	-0.0555	-0.3648	0.8125	-0.3779	0.6661	-33.389	-7.862	-23.585
19	6.1567	0.5036	2.9392	5.2792	2.3914	9.0591	-0.2018	0.3043	-0.0425	-0.1875	0.0416	0.1465	0.3689	-0.2493	0.1602	0.6	-0.0139	-0.2869	0.5575	-0.2878	0.4987	-32.367	-4.321	-20.952
20	1.4286	1.3988	2.5162	6.884	5.5023	6.113	0.0566	-0.1034	-0.0375	-0.0754	0.056	-0.1841	0.0202	-0.1602	-0.1126	0.6139	-0.0183	-0.2191	0.6707	-0.1783	0.4609	-29.017	1.576	-13.199
21	9.4842	-8.4368	8.3018	30.1057	-3.386	8.0778	1.1101	0.4333	-1.376	-0.2989	0.1346	0.1222	1.4603	0.4384	-1.2447	1.7315	0.122	0.0345	0.1474	-0.3323	0.8455	-27.257	-60.204	-11.282
22	2.6394	1.2597	2.2279	20.1173	-3.2131	10.2733	0.4648	0.5829	-2.448	-3.1314	-0.131	0.6146	3.4832	-0.5556	-0.3338	2.1359	-0.0874	0.0687	0.3472	-0.8915	3.0646	-32.462	-51.163	-11.117
23	12.3481	4.7595	-2.0471	13.5492	-13.4061	22.1938	0.163	0.5709	-2.5238	-1.4568	-0.1274	-0.2701	2.2073	0.5856	-0.0356	1.2101	0.1994	0.1081	0.2458	-0.4246	1.1978	-27.816	-47.056	-5.398
24	8.4398	1.7028	-2.133	18.1071	-0.4816	8.3479	0.2736	0.2695	-1.3954	-1.6813	-0.3827	0.1158	1.879	-0.1115	0.1091	1.2744	0.0897	-0.008	0.278	-0.4473	0.9233	-31.028	-42.894	-5.576
25	7.3737	-4.3967	-0.425	12.2494	-0.6168	3.141	-0.0317	0.9699	-1.764	-0.6415	-0.3976	0.0217	0.5128	-0.014	0.4293	1.1418	0.0647	0.0126	0.4607	-0.4617	0.7406	-31.98	-38.182	-4.838
26	21.126	7.6505	20.4743	36.7564	-2.1737	22.5487	-0.5909	-0.6352	-0.117	0.5672	0.7494	0.1089	-0.7677	-0.8917	-0.1586	0.7219	0.0251	0.0302	0.3174	-0.5082	1.0188	-38.056	-34.717	-3.379
27	5.3105	2.1534	1.0803	4.7869	1.9211	12.8498	0.0759	-0.0058	-1.0036	-0.2892	-0.0092	-0.718	0.4445	-0.0321	-0.0668	0.9816	0.2171	0.1912	0.3019	-0.2296	0.7244	-28.814	-33.446	-0.954
28	4.6514	1.8207	0.3388	14.5306	4.1165	5.9753	0.2346	0.1557	-0.5426	-0.6764	-0.2544	0.0137	0.5361	-0.0392	0.0198	0.7465	0.1017	0.066	0.4745	-0.28	0.5887	-31.654	-26.261	0.683
29	42.7305	16.1672	9.0276	18.731	-1.6817	11.9496	-0.1371	0.1488	-3.6951	1.2745	0.4831	-0.3881	-0.3584	-0.2605	-0.3459	0.5117	0.1323	0.2574	0.3485	-0.1142	0.7107	-34.964	-23.585	8.672
30	0.1288	1.2612	0.3558	14.5885	1.9701	2.5068	-0.0833	-0.0124	-0.0077	-0.2315	-0.2393	0.0541	-0.3243	-0.2469	0.3226	0.5268	0.02	0.2325	0.5856	-0.2116	0.4353	-30.579	-12.068	4.856

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 26
2	X-RAY DIFFRACTION	2	A	27 - 66
3	X-RAY DIFFRACTION	3	A	67 - 78
4	X-RAY DIFFRACTION	4	A	79 - 147
5	X-RAY DIFFRACTION	5	A	148 - 174
6	X-RAY DIFFRACTION	6	A	175 - 184
7	X-RAY DIFFRACTION	7	A	185 - 204
8	X-RAY DIFFRACTION	8	A	205 - 215
9	X-RAY DIFFRACTION	9	A	216 - 224
10	X-RAY DIFFRACTION	10	A	225 - 241
11	X-RAY DIFFRACTION	11	B	21 - 35
12	X-RAY DIFFRACTION	12	B	36 - 55
13	X-RAY DIFFRACTION	13	B	56 - 76
14	X-RAY DIFFRACTION	14	B	77 - 95
15	X-RAY DIFFRACTION	15	B	96 - 125
16	X-RAY DIFFRACTION	16	B	126 - 143
17	X-RAY DIFFRACTION	17	B	144 - 164
18	X-RAY DIFFRACTION	18	B	165 - 184
19	X-RAY DIFFRACTION	19	B	185 - 204
20	X-RAY DIFFRACTION	20	B	205 - 241
21	X-RAY DIFFRACTION	21	C	21 - 36
22	X-RAY DIFFRACTION	22	C	37 - 66
23	X-RAY DIFFRACTION	23	C	67 - 80
24	X-RAY DIFFRACTION	24	C	81 - 100
25	X-RAY DIFFRACTION	25	C	101 - 121
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