PDB-6ugb: C3 symmetric peptide design number 2, Baby Basil

ID or keywords:

Entry

Database: PDB / ID: 6ugb

Title

C3 symmetric peptide design number 2, Baby Basil

Components

C3 symmetric peptide design number 2, Baby Basil

Keywords

DE NOVO PROTEIN / cyclic peptide / 3-fold symmetric / racemic mixture

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å

Model details

S2 symmetric cyclic peptide

Authors

Mulligan, V.K. / Kang, C.S. / Antselovich, I. / Sawaya, M.R. / Yeates, T.O. / Baker, D.

Funding support

United States, 2items

Citation

Journal: Protein Sci. / Year: 2020
Title: Computational design of mixed chirality peptide macrocycles with internal symmetry.
Authors: Mulligan, V.K. / Kang, C.S. / Sawaya, M.R. / Rettie, S. / Li, X. / Antselovich, I. / Craven, T.W. / Watkins, A.M. / Labonte, J.W. / DiMaio, F. / Yeates, T.O. / Baker, D.

History

Deposition	Sep 26, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 2, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ugb.cif.gz	17.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ugb.ent.gz	9.8 KB	Display	PDB format
PDBx/mmJSON format	6ugb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ugb_validation.pdf.gz	372.9 KB	Display	wwPDB validaton report
Full document	6ugb_full_validation.pdf.gz	372.8 KB	Display
Data in XML	6ugb_validation.xml.gz	2.2 KB	Display
Data in CIF	6ugb_validation.cif.gz	2.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ug/6ugb ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ugb	HTTPS FTP

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Related structure data

Related structure data	6ucxC 6ud9C 6udrC 6udwC 6udzC 6uf4C 6uf7C 6uf8C 6uf9C 6ufaC 6ufuC 6ug2C 6ug3C 6ug6C 6ugcC C: citing same article (ref.)

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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: C3 symmetric peptide design number 2, Baby Basil

B: C3 symmetric peptide design number 2, Baby Basil

hetero molecules

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

1

A: C3 symmetric peptide design number 2, Baby Basil

hetero molecules

A: C3 symmetric peptide design number 2, Baby Basil

hetero molecules

A: C3 symmetric peptide design number 2, Baby Basil

hetero molecules

defined by author
1.3 kDa, 3 polymers

2

B: C3 symmetric peptide design number 2, Baby Basil

hetero molecules

B: C3 symmetric peptide design number 2, Baby Basil

hetero molecules

B: C3 symmetric peptide design number 2, Baby Basil

hetero molecules

defined by author
1.64 kDa, 3 polymers

Unit cell

Length a, b, c (Å)	24.720, 24.720, 19.590
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	147
Space group name H-M	P-3

Components on special symmetry positions

ID	Model	Components
1	1	A-101- NA
2	1	A-102- NA
3	1	B-104- NA

#1: Protein/peptide	C3 symmetric peptide design number 2, Baby Basil Mass: 387.412 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The crystal contains a racemic mixture of the peptide. Chain A corresponds to 1/3 of the cyclic peptide. Chain B corresponds to 1/3 of another copy of the cyclic peptide. Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.89 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M zinc acetate, 0.1 M imidazole pH 8.0, 2.5 M sodium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.7749 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2018

Radiation

Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.7749 Å / Relative weight: 1

Reflection

Resolution: 0.95→21.41 Å / Num. obs: 7972 / % possible obs: 94.1 % / Redundancy: 2.865 % / B_iso Wilson estimate: 11.649 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.063 / R_rim(I) all: 0.075 / Χ²: 0.908 / Net I/σ(I): 8.44

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
0.95-0.97	2.531	1.122	1.16	591	0.393	1.398	95.3
0.97-1	2.699	0.949	1.42	589	0.695	1.175	96.4
1-1.03	2.55	0.589	2.15	567	0.869	0.733	94.7
1.03-1.06	2.673	0.44	3.08	572	0.882	0.542	98.6
1.06-1.1	2.825	0.274	4.66	538	0.943	0.337	96.8
1.1-1.13	2.884	0.25	5.21	518	0.957	0.304	97
1.13-1.18	2.895	0.192	6.02	522	0.966	0.233	96.5
1.18-1.23	2.762	0.154	6.66	462	0.978	0.189	93.9
1.23-1.28	2.648	0.125	7.87	452	0.985	0.153	95.4
1.28-1.34	3.092	0.103	9.11	433	0.989	0.123	95.8
1.34-1.42	3.014	0.082	11.33	428	0.989	0.099	93.9
1.42-1.5	3.054	0.065	13.04	387	0.993	0.079	93.7
1.5-1.6	3	0.063	14.62	348	0.992	0.075	92.8
1.6-1.73	2.824	0.054	14.02	319	0.995	0.065	88.1
1.73-1.9	3.165	0.047	18.07	310	0.996	0.056	90.9
1.9-2.12	3.282	0.049	18.7	287	0.995	0.059	92.3
2.12-2.45	3.22	0.05	19.38	232	0.996	0.059	87.9
2.45-3	3.213	0.042	20.68	188	0.999	0.05	87.4
3-4.25	3.066	0.044	21.14	151	0.995	0.052	83
4.25-21.41	3.667	0.049	23.32	78	0.996	0.057	82.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0266	refinement
XDS	20180126	data reduction
XSCALE	20180126	data scaling
PDB_EXTRACT	3.25	data extraction
SHELXD	SHELXT actually	phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 0.95→21.408 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.981 / WR_factor R_free: 0.176 / WR_factor R_work: 0.16 / SU B: 0.287 / SU ML: 0.007 / Average fsc free: 0.9691 / Average fsc work: 0.9691 / Cross valid method: FREE R-VALUE / ESU R: 0.017 / ESU R Free: 0.017
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.1618	834	10.483 %
R_work	0.1593	7122	-
all	0.16	-	-
obs	-	7956	94.265 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 13.336 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.38 Å²	0.19 Å²	-0 Å²
2-	-	0.38 Å²	0 Å²
3-	-	-	-1.234 Å²

Refinement step

Cycle: LAST / Resolution: 0.95→21.408 Å /

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	52	0	6	8	66

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	59
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	59
X-RAY DIFFRACTION	r_angle_refined_deg	1.88	1.847	75
X-RAY DIFFRACTION	r_angle_other_deg	0.447	1.626	136
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.747	5	4
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.423	15	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.844	15	11
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.716	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	7
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	54
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	19
X-RAY DIFFRACTION	r_nbd_refined	0.452	0.2	9
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.229	0.2	29
X-RAY DIFFRACTION	r_nbtor_refined	0.14	0.2	17
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	19
X-RAY DIFFRACTION	r_metal_ion_refined	0.115	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.745	0.2	32
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.464	0.2	3
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.033	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.909	1.021	22
X-RAY DIFFRACTION	r_mcbond_other	0.907	1.031	21
X-RAY DIFFRACTION	r_mcangle_it	1.286	1.566	24
X-RAY DIFFRACTION	r_mcangle_other	1.26	1.549	25
X-RAY DIFFRACTION	r_scbond_it	2.123	1.276	37
X-RAY DIFFRACTION	r_scbond_other	2.177	1.303	35
X-RAY DIFFRACTION	r_scangle_it	2.511	1.842	51
X-RAY DIFFRACTION	r_scangle_other	2.511	1.839	51
X-RAY DIFFRACTION	r_lrange_it	1.703	9.958	54
X-RAY DIFFRACTION	r_lrange_other	1.809	9.477	46
X-RAY DIFFRACTION	r_rigid_bond_restr	0.865	3	118

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
0.95-0.975	0.605	62	0.567	517	0.571	591	0.868	0.857	97.9695	0.515
0.975-1.001	0.486	84	0.533	517	0.526	623	0.923	0.892	96.4687	0.461
1.001-1.03	0.349	48	0.364	504	0.363	584	0.946	0.945	94.5205	0.294
1.03-1.062	0.239	66	0.244	505	0.244	579	0.973	0.97	98.6183	0.189
1.062-1.097	0.174	66	0.188	474	0.187	558	0.984	0.983	96.7742	0.152
1.097-1.135	0.163	45	0.168	475	0.168	536	0.982	0.988	97.0149	0.144
1.135-1.178	0.181	47	0.162	471	0.164	537	0.983	0.99	96.4618	0.141
1.178-1.226	0.179	39	0.147	423	0.149	492	0.982	0.991	93.9024	0.129
1.226-1.28	0.159	48	0.133	400	0.136	470	0.99	0.992	95.3192	0.118
1.28-1.342	0.11	31	0.12	406	0.119	456	0.992	0.993	95.8333	0.108
1.342-1.414	0.118	37	0.089	380	0.091	444	0.993	0.995	93.9189	0.085
1.414-1.5	0.077	49	0.089	341	0.087	417	0.997	0.996	93.5252	0.09
1.5-1.603	0.101	40	0.083	316	0.085	383	0.994	0.996	92.9504	0.089
1.603-1.73	0.139	17	0.106	298	0.108	358	0.992	0.994	87.9888	0.12
1.73-1.894	0.116	48	0.107	266	0.109	345	0.993	0.994	91.0145	0.135
1.894-2.116	0.104	27	0.133	248	0.129	299	0.994	0.991	91.9732	0.175
2.116-2.439	0.18	40	0.136	204	0.143	275	0.981	0.99	88.7273	0.181
2.439-2.978	0.098	22	0.147	162	0.138	212	0.996	0.988	86.7924	0.222
2.978-4.171	0.189	8	0.176	139	0.176	176	0.985	0.982	83.5227	0.25
4.171-21.408	0.334	10	0.266	76	0.273	105	0.958	0.962	81.9048	0.428

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