PDB-4ydt: Beta1 synthetic solenoid protein

ID or keywords:

Entry

Database: PDB / ID: 4ydt

Title

Beta1 synthetic solenoid protein

Components

beta1 protein

Keywords

STRUCTURAL PROTEIN / solenoid / scaffold

Function / homology

E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.31 Å

Authors

Murray, J.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	Feb 23, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 9, 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	4ydt.cif.gz	172.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ydt.ent.gz	141.8 KB	Display	PDB format
PDBx/mmJSON format	4ydt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yd/4ydt ftp://data.pdbj.org/pub/pdb/validation_reports/yd/4ydt	HTTPS FTP

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Related structure data

Related structure data	4yc5C 4ycqC 4yeiC 4yfoC 5di5C 5dn0C 5dnsC 5dqaC 5draC 5dzbC C: citing same article (ref.)
Similar structure data	5dqa-2 4yc5-1 5dqa-1 2wng-d 3qc6-d 5n40-d 6h9m-d 5dqa-3 3okq-1 4mkm-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

Deposited unit

A: beta1 protein

B: beta1 protein

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

1

A: beta1 protein

B: beta1 protein

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

2

B: beta1 protein

A: beta1 protein

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

Unit cell

Length a, b, c (Å)	102.370, 102.370, 290.430
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 20 - 234 / Label seq-ID: 20 - 234

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	beta1 protein Mass: 24676.037 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.97 Å³/Da / Density % sol: 58.55 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 160 mM magnesium chloride, 80 mM sodium cacodylate pH 6.5, 40% v/v PEG 200 PH range: 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0403 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0403 Å / Relative weight: 1
Reflection	Resolution: 3.31→75.67 Å / Num. all: 8605 / Num. obs: 8605 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.71 % / R_merge(I) obs: 0.16 / Net I/av σ(I): 13.0217 / Net I/σ(I): 5.2363
Reflection shell	Resolution: 3.31→3.4 Å / Redundancy: 7.92 % / R_merge(I) obs: 0.95 / Mean I/σ(I) obs: 1.08 / % possible all: 96.87

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Resolution: 3.31→75.67 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.887 / SU B: 67.22 / SU ML: 0.459 / Cross valid method: THROUGHOUT / ESU R Free: 0.647 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30299	405	4.7 %	RANDOM
R_work	0.25487	-	-	-
obs	0.2571	8200	94.8 %	-

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: 91.885 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.35 Å²	2.17 Å²	-0 Å²
2-	-	4.35 Å²	-0 Å²
3-	-	-	-14.1 Å²

Refinement step

Cycle: 1 / Resolution: 3.31→75.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3170	0	0	0	3170

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	3218
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	3048
X-RAY DIFFRACTION	r_angle_refined_deg	1.564	1.939	4376
X-RAY DIFFRACTION	r_angle_other_deg	1.048	3	6918
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.527	5	432
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.243	25.581	172
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.803	15	498
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.476	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	512
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3942
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	774
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	1.996	4.767	1728
X-RAY DIFFRACTION	r_mcbond_other	1.996	4.768	1727
X-RAY DIFFRACTION	r_mcangle_it	3.245	7.156	2160
X-RAY DIFFRACTION	r_mcangle_other	3.244	7.155	2161
X-RAY DIFFRACTION	r_scbond_it	2.56	5.114	1489
X-RAY DIFFRACTION	r_scbond_other	2.559	5.113	1490
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.152	7.552	2217
X-RAY DIFFRACTION	r_long_range_B_refined	7.142	46.39	14338
X-RAY DIFFRACTION	r_long_range_B_other	7.142	46.391	14337
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 26740 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.02 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 3.312→3.398 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.374	29	-
R_work	0.332	604	-
obs	-	-	96.94 %

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	1.451	-1.5265	2.6792	4.9206	4.2881	20.573	-0.5447	-0.7581	-0.0778	1.6313	1.0901	-0.0866	0.9198	-0.2408	-0.5454	0.8458	-0.0896	-0.0198	1.1449	-0.0154	0.4826	-35.63	103.673	132.376
2	8.4646	2.7957	-2.1596	3.8876	2.082	12.2255	0.2127	-1.0491	0.1549	0.8899	-0.263	0.4316	0.1607	-0.3042	0.0503	0.5602	-0.2578	-0.0723	0.6529	0.0053	0.4278	-41.231	105.696	124.074
3	10.5049	-1.4328	6.4733	10.5905	7.2554	10.3821	-0.2955	-1.3843	0.1496	0.7339	0.2155	-0.042	0.4394	-0.7342	0.08	0.5748	-0.1389	-0.0362	0.6671	0.1887	0.2133	-38.104	101.992	117.9
4	7.1797	2.7173	0.7606	12.4889	3.1939	9.2597	0.3343	-0.3315	-0.1049	0.5521	-0.2307	0.1402	0.3002	0.1345	-0.1036	0.3281	-0.2255	-0.1641	0.2276	0.0236	0.2493	-40.589	104.179	111.883
5	12.2111	1.5638	-0.2198	2.5565	4.6469	15.0649	-0.315	-1.1368	0.993	-0.3546	0.0005	0.3587	-0.3559	0.6551	0.3145	0.3039	-0.1046	-0.2712	0.2058	0.016	0.4181	-42.283	107.598	105.653
6	5.7772	-1.7633	2.1002	3.6337	2.0087	12.7242	0.2261	-0.0221	-0.1022	-0.1274	-0.1324	0.0859	0.5988	-0.4273	-0.0937	0.2539	-0.0766	-0.1315	0.0334	0.0431	0.3374	-43.125	102.1	98.055
7	7.4595	11.6245	9.8723	28.4676	-0.5969	37.7675	0.1497	0.3445	0.091	0.8261	-0.2078	0.0976	-0.6954	1.5816	0.0581	0.3505	-0.1717	-0.1529	0.1357	0.1336	0.5713	-40.891	110.828	91.096
8	14.6809	3.3342	6.9515	1.2967	2.9653	12.8083	-0.2263	0.7527	0.2979	0.0582	0.1954	-0.197	1.3644	-0.1973	0.0309	0.5283	-0.1722	-0.118	0.119	-0.0098	0.3199	-42.12	96.866	89.263
9	6.9391	0.3971	-2.9352	0.0763	0.6126	13.2159	0.3532	0.126	0.0616	0.0761	-0.0235	-0.0182	0.3719	-0.2662	-0.3297	0.2689	-0.0196	-0.1257	0.056	-0.0177	0.3826	-44.852	100.645	82.755
10	14.929	8.6476	5.4053	28.8066	12.8175	29.0515	0.6926	-0.4391	-1.2145	0.2414	0.5223	0.3142	0.9124	-2.16	-1.2149	0.1825	-0.1227	-0.2259	0.5845	0.1445	0.5302	-49.733	103.053	72.445
11	21.9615	-16.7945	6.5224	12.8962	-6.0592	26.0999	-1.1502	-0.692	-0.7235	0.9743	0.5009	0.4928	-1.6361	-1.0675	0.6494	0.6825	-0.3943	-0.06	1.0089	-0.0024	0.6004	-88.454	77.61	175.336
12	22.4081	-6.3713	7.7901	10.0646	1.0932	10.9123	0.3254	-1.0535	-0.7604	1.6378	-0.2091	-0.2217	0.8439	-0.2912	-0.1163	0.7553	-0.2119	-0.1078	0.8385	0.0955	0.2227	-88.991	70.169	171.559
13	9.6638	-1.6335	-0.1257	10.0462	0.9599	13.4267	0.1851	-0.8351	0.3875	0.6965	-0.2493	-0.1472	0.1576	-0.2689	0.0642	0.38	-0.3015	-0.1677	0.5271	-0.0182	0.2303	-89.571	76.778	163.505
14	9.0174	2.9792	-3.9019	7.802	7.0817	11.9701	0.6219	-1.558	0.1909	0.8672	-0.8988	0.319	0.5214	0.2116	0.2769	0.4315	-0.4846	-0.2202	0.7596	0.0941	0.3667	-93.845	76.3	158.539
15	8.4723	1.5252	2.9756	9.5183	4.7075	8.1239	0.1626	-0.3484	0.0796	0.07	-0.2801	0.4356	0.1492	-0.3572	0.1176	0.3728	-0.2344	-0.151	0.3188	0.008	0.2346	-93.097	74.662	151.981
16	9.1671	0.6594	1.7515	4.0238	-0.9821	12.5477	0.009	-0.3096	-0.1152	0.3544	-0.129	0.1486	-0.0923	-0.3893	0.12	0.342	-0.1548	-0.1544	0.1604	-0.0376	0.2786	-93.924	73.581	142.844
17	12.4164	-3.9911	0.8383	15.6738	-3.0167	12.18	0.735	-0.9	-0.5627	-0.7508	-0.1193	-0.1852	0.182	0.1334	-0.6157	0.3283	-0.0524	-0.1207	0.1115	0.015	0.1617	-93.348	72.106	136.089
18	16.6868	-13.9456	0.8252	35.5086	2.8944	11.4011	-0.7563	0.0302	1.2907	1.5217	0.7442	-1.0039	-0.9194	1.2643	0.0121	0.2713	-0.135	-0.1384	0.1768	0.0319	0.2146	-90.932	76.687	132.496
19	5.0662	2.859	-0.1861	3.224	4.6923	15.818	0.3368	-0.537	-0.1007	0.0298	-0.3256	-0.1158	0.392	-0.1865	-0.0112	0.5972	-0.08	-0.0581	0.1049	0.0043	0.3755	-96.44	70.248	126.554
20	39.7464	-0.1143	20.9908	8.8736	-8.7557	24.0681	-0.3797	0.2654	0.1059	0.0451	-0.1151	0.9354	-0.6646	-0.8685	0.4948	0.2526	0.0945	-0.0616	0.3665	-0.2677	0.6222	-100.399	73.398	116.031

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	20 - 36
2	X-RAY DIFFRACTION	2	A	37 - 68
3	X-RAY DIFFRACTION	3	A	69 - 82
4	X-RAY DIFFRACTION	4	A	83 - 119
5	X-RAY DIFFRACTION	5	A	120 - 133
6	X-RAY DIFFRACTION	6	A	134 - 185
7	X-RAY DIFFRACTION	7	A	186 - 191
8	X-RAY DIFFRACTION	8	A	192 - 201
9	X-RAY DIFFRACTION	9	A	202 - 227
10	X-RAY DIFFRACTION	10	A	228 - 234
11	X-RAY DIFFRACTION	11	B	20 - 29
12	X-RAY DIFFRACTION	12	B	30 - 42
13	X-RAY DIFFRACTION	13	B	43 - 77
14	X-RAY DIFFRACTION	14	B	78 - 91
15	X-RAY DIFFRACTION	15	B	92 - 128
16	X-RAY DIFFRACTION	16	B	129 - 167
17	X-RAY DIFFRACTION	17	B	168 - 185
18	X-RAY DIFFRACTION	18	B	186 - 196
19	X-RAY DIFFRACTION	19	B	197 - 224
20	X-RAY DIFFRACTION	20	B	225 - 234

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