PDB-4yfo: beta1_ex1

ID or keywords:

Entry

Database: PDB / ID: 4yfo

Title

beta1_ex1

Components

beta1_ex1

Keywords

DE NOVO PROTEIN / synthetic protein / solenoid

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: 3.39 Å

Authors

Murray, J.W. / MacDonald, J.T.

Funding support

United Kingdom, 1items

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 25, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2016	Group: Database references
Revision 1.2	Aug 30, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	May 8, 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	4yfo.cif.gz	100.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4yfo_validation.pdf.gz	424.4 KB	Display	wwPDB validaton report
Full document	4yfo_full_validation.pdf.gz	426.4 KB	Display
Data in XML	4yfo_validation.xml.gz	10.2 KB	Display
Data in CIF	4yfo_validation.cif.gz	12.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yf/4yfo ftp://data.pdbj.org/pub/pdb/validation_reports/yf/4yfo	HTTPS FTP

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Related structure data

Related structure data	4yc5C 4ycqC 4ydtC 4yeiC 5di5C 5dn0C 5dnsC 5dqaC 5draC 5dzbC C: citing same article (ref.)
Similar structure data	5dzb-2 5dzb-1 5dzb-3 3onx-d 6bg9-d 6fpd-1 5mw5-d 4nn0-d 6tgz-d 5mwf-6 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: beta1_ex1

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

1

A: beta1_ex1

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

Unit cell

Length a, b, c (Å)	105.180, 105.180, 323.500
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

#1: Protein	beta1_ex1 Mass: 26864.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli KRX (bacteria)

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 6.41 Å³/Da / Density % sol: 80.81 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 90 mM Bis Tris pH 5.5, 2.7 M sodium chloride / PH range: 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 26, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 3.39→107.83 Å / Num. all: 9607 / Num. obs: 9607 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / R_merge(I) obs: 0.129 / Net I/av σ(I): 14.3 / Net I/σ(I): 14.3
Reflection shell	Resolution: 3.39→3.48 Å / Redundancy: 9.1 % / R_merge(I) obs: 0.585 / Mean I/σ(I) obs: 4.3 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0107	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Resolution: 3.39→39.68 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.924 / SU B: 34.523 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.538 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23339	478	4.8 %	RANDOM
R_work	0.19556	-	-	-
obs	0.19733	9477	96.66 %	-

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: 113.294 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.58 Å²	2.79 Å²	0 Å²
2-	-	5.58 Å²	0 Å²
3-	-	-	-18.11 Å²

Refinement step

Cycle: LAST / Resolution: 3.39→39.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1702	0	0	0	1702

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.019	1716
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1630
X-RAY DIFFRACTION	r_angle_refined_deg	2.522	1.947	2330
X-RAY DIFFRACTION	r_angle_other_deg	1.243	3	3703
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.797	5	232
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.38	25.889	90
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.712	15	267
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.122	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	273
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2101
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	403
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	4.054	6.978	931
X-RAY DIFFRACTION	r_mcbond_other	4.007	6.981	930
X-RAY DIFFRACTION	r_mcangle_it	6.257	10.469	1162
X-RAY DIFFRACTION	r_mcangle_other	6.261	10.468	1163
X-RAY DIFFRACTION	r_scbond_it	6.204	7.724	785
X-RAY DIFFRACTION	r_scbond_other	6.2	7.723	786
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.503	11.33	1169
X-RAY DIFFRACTION	r_long_range_B_refined	12.693	68.142	7660
X-RAY DIFFRACTION	r_long_range_B_other	12.701	68.141	7661
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.35→3.436 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	32	-
R_work	0.366	698	-
obs	-	-	97.72 %

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	18.1124	-1.8815	-12.3077	0.1984	1.2783	8.365	0.1262	-1.1854	0.2399	0.0039	0.0669	-0.0352	-0.1285	0.7923	-0.1931	1.5988	0.0605	-0.0996	0.9076	0.2905	0.485	-43.879	8.135	8.112
2	28.9422	21.9634	-13.4772	16.7062	-10.2149	6.2846	0.9134	-1.2449	-0.4505	0.9224	-1.0306	-0.4373	-0.3958	0.5579	0.1172	1.9473	0.1501	-0.3596	1.0753	-0.059	0.794	-51.887	6.975	8.574
3	4.1234	-0.5082	0.4898	3.7064	-1.1109	13.4766	0.1111	-0.2911	0.2175	1.131	-0.4997	-0.2616	-0.5587	0.6607	0.3887	0.97	0.0357	0.0039	0.4112	0.1761	0.1691	-44.656	12.778	0.099
4	46.6116	-4.0066	0.4289	11.8697	-10.3424	15.6123	0.7471	-1.4579	-0.5567	0.3162	-0.7112	0.2403	1.1644	-0.032	-0.0359	0.7734	0.0378	0.1673	0.4045	0.0892	0.0643	-46.341	4.485	-6.822
5	10.0546	0.898	2.3992	14.5615	-4.0001	14.2082	-0.2821	-0.2112	0.3244	1.978	0.0984	0.3415	-0.2057	-0.4018	0.1837	0.7024	0.0778	0.0825	0.1945	0.0969	0.0827	-46.423	14.155	-9.277
6	22.7365	17.144	7.7038	44.2062	18.5804	16.2007	-0.8193	-1.3613	0.5112	0.6527	-0.3619	-0.374	-0.0946	0.2781	1.1812	0.6482	0.2146	-0.1383	0.5744	0.0237	0.2398	-37.507	12.454	-13.495
7	4.7447	0.7871	0.0823	8.0865	-0.8478	12.8165	-0.1317	-0.2963	0.0674	0.5689	-0.1639	-0.2088	0.5372	0.4234	0.2956	0.3669	0.0996	0.056	0.1762	0.1466	0.1491	-44.315	13.732	-22.251
8	12.799	-0.5631	2.2823	4.6724	-1.8879	11.6477	-0.2967	-0.1619	0.0995	0.4627	0.1363	0.0756	0.2324	-0.0008	0.1604	0.165	0.0257	0.0396	0.0983	0.0923	0.0976	-45.253	16.86	-33.688
9	30.373	-2.678	1.884	13.3765	-0.7288	8.7174	0.2951	-0.9955	-1.5451	-0.0598	-0.0763	-0.4694	1.1023	0.4764	-0.2188	0.4213	0.1204	0.0716	0.2173	0.0981	0.1524	-43.293	11.91	-38.967
10	1.5773	1.4411	-1.0812	2.5123	-3.1912	14.0208	-0.0697	-0.0212	-0.0955	-0.304	-0.1094	-0.1315	-0.0617	0.4094	0.1791	0.1229	0.0584	0.0754	0.1332	0.0281	0.2068	-44.791	19.929	-47.364

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 27
2	X-RAY DIFFRACTION	2	A	28 - 34
3	X-RAY DIFFRACTION	3	A	35 - 66
4	X-RAY DIFFRACTION	4	A	67 - 73
5	X-RAY DIFFRACTION	5	A	74 - 102
6	X-RAY DIFFRACTION	6	A	103 - 108
7	X-RAY DIFFRACTION	7	A	109 - 172
8	X-RAY DIFFRACTION	8	A	173 - 204
9	X-RAY DIFFRACTION	9	A	205 - 216
10	X-RAY DIFFRACTION	10	A	217 - 253

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