PDB-6ufa: S4 symmetric peptide design number 1, Tim zinc-bound form

ID or keywords:

Entry

Database: PDB / ID: 6ufa

Title

S4 symmetric peptide design number 1, Tim zinc-bound form

Components

S4-1, Tim, Zinc-bound form

Keywords

DE NOVO PROTEIN / cyclic peptide / centrosymmetric macrocycle / L and D-amino acids

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 0.77 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 24, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 2, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 2, 2025	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	6ufa.cif.gz	33.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6ufa.ent.gz	22.7 KB	Display	PDB format
PDBx/mmJSON format	6ufa.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ufa_validation.pdf.gz	372.6 KB	Display	wwPDB validaton report
Full document	6ufa_full_validation.pdf.gz	372.6 KB	Display
Data in XML	6ufa_validation.xml.gz	3.2 KB	Display
Data in CIF	6ufa_validation.cif.gz	3.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uf/6ufa ftp://data.pdbj.org/pub/pdb/validation_reports/uf/6ufa	HTTPS FTP

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Related structure data

Related structure data	6ucxC 6ud9C 6udrC 6udwC 6udzC 6uf4C 6uf7C 6uf8C 6uf9C 6ufuC 6ug2C 6ug3C 6ug6C 6ugbC 6ugcC C: citing same article (ref.)
Similar structure data	1hp9-d 5kwo-d 6nw8-d 2lix-d 6m6j-d 5kx0-d 2mn1-d 1tck-d 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: S4-1, Tim, Zinc-bound form

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	20.960, 20.980, 26.880
Angle α, β, γ (deg.)	106.103, 94.813, 89.429
Int Tables number	2
Space group name H-M	P-1

#1: Protein/peptide	S4-1, Tim, Zinc-bound form Mass: 2907.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ab initio design / Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 35 / 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: 1.95 Å³/Da / Density % sol: 36.79 % / Description: square plate
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.1 M sodium malonate, 0.1 M HEPES, pH 7, 0.5% (w/v) Jeffamine ED-2003

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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: 0.7293 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.7293 Å / Relative weight: 1

Reflection

Resolution: 0.77→20.88 Å / Num. obs: 46103 / % possible obs: 88.7 % / Redundancy: 3.597 % / B_iso Wilson estimate: 7.559 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.039 / R_rim(I) all: 0.046 / Χ²: 1.093 / Net I/σ(I): 15.3

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
0.77-0.79	3.244	0.236	3.95	2954	0.962	0.283	77.2
0.79-0.81	3.631	0.202	5.05	3320	0.974	0.236	87.9
0.81-0.84	3.564	0.159	6.17	3240	0.982	0.186	88.6
0.84-0.86	3.405	0.141	6.63	3109	0.985	0.167	88.6
0.86-0.89	3.707	0.117	8.38	3092	0.991	0.137	89.9
0.89-0.92	3.696	0.089	10.63	2949	0.994	0.104	89.5
0.92-0.96	3.567	0.073	12.33	2886	0.995	0.085	88.9
0.96-0.99	3.554	0.065	14.2	2745	0.996	0.077	89.1
0.99-1.04	3.771	0.061	15.88	2660	0.997	0.071	90.6
1.04-1.09	3.711	0.054	17.55	2561	0.997	0.063	90.8
1.09-1.15	3.643	0.048	19.46	2383	0.997	0.056	88.9
1.15-1.22	3.591	0.043	21.62	2201	0.998	0.051	87.2
1.22-1.3	3.768	0.042	22.95	2241	0.998	0.048	93.1
1.3-1.41	3.728	0.039	24.8	2036	0.998	0.046	91.1
1.41-1.54	3.637	0.038	25.71	1824	0.998	0.044	90.4
1.54-1.72	3.523	0.035	27.09	1579	0.998	0.041	85.5
1.72-1.99	3.581	0.034	29.2	1529	0.998	0.039	94.6
1.99-2.43	3.53	0.035	30.7	1286	0.998	0.041	92.5
2.43-3.44	3.415	0.033	31.13	918	0.998	0.038	86.3
3.44-20.88	3.611	0.035	32.86	573	0.997	0.041	98.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
XDS	20180126	data reduction
XSCALE	20180126	data scaling
PDB_EXTRACT	3.25	data extraction
SHELXT		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 0.77→20.001 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.979 / WR_factor R_free: 0.137 / WR_factor R_work: 0.13 / SU B: 0.08 / SU ML: 0.003 / Average fsc free: 0.9909 / Average fsc work: 0.9917 / Cross valid method: FREE R-VALUE / ESU R: 0.008 / ESU R Free: 0.009
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1318	4610	9.999 %
R_work	0.1263	41493	-
all	0.127	-	-
obs	-	46103	88.789 %

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: 8.627 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.086 Å²	0.006 Å²	-0.031 Å²
2-	-	0.049 Å²	-0.005 Å²
3-	-	-	0.039 Å²

Refinement step

Cycle: LAST / Resolution: 0.77→20.001 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	204	0	1	35	240

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	222
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	218
X-RAY DIFFRACTION	r_angle_refined_deg	1.594	1.646	306
X-RAY DIFFRACTION	r_angle_other_deg	0.499	1.574	504
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.619	5	28
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	53.282	27.143	7
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.017	10	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	8.12	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	22
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	268
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	46
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	65
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.238	0.2	196
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	104
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	103
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	11
X-RAY DIFFRACTION	r_metal_ion_refined	0.04	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.085	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.115	0.2	13
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.055	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	0.639	0.54	100
X-RAY DIFFRACTION	r_mcbond_other	0.638	0.539	100
X-RAY DIFFRACTION	r_mcangle_it	0.944	0.818	126
X-RAY DIFFRACTION	r_mcangle_other	0.94	0.817	127
X-RAY DIFFRACTION	r_scbond_it	1.552	0.878	120
X-RAY DIFFRACTION	r_scbond_other	1.546	0.875	121
X-RAY DIFFRACTION	r_scangle_it	2.138	1.191	178
X-RAY DIFFRACTION	r_scangle_other	2.132	1.187	179
X-RAY DIFFRACTION	r_lrange_it	1.874	8.181	239
X-RAY DIFFRACTION	r_lrange_other	1.776	7.839	234
X-RAY DIFFRACTION	r_rigid_bond_restr	1.231	3	438

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
0.77-0.79	0.189	295	0.18	2653	0.181	3823	0.976	0.98	77.1122	0.134
0.79-0.812	0.155	331	0.145	2986	0.146	3764	0.986	0.986	88.1243	0.11
0.812-0.835	0.133	324	0.129	2914	0.129	3653	0.989	0.989	88.6395	0.097
0.835-0.861	0.137	310	0.125	2785	0.126	3496	0.989	0.99	88.5297	0.095
0.861-0.889	0.12	309	0.106	2786	0.107	3435	0.991	0.993	90.1019	0.083
0.889-0.92	0.094	295	0.089	2650	0.09	3289	0.995	0.995	89.5409	0.073
0.92-0.955	0.094	288	0.086	2595	0.087	3233	0.995	0.996	89.1741	0.073
0.955-0.994	0.083	274	0.079	2469	0.08	3075	0.996	0.996	89.2032	0.071
0.994-1.038	0.087	266	0.079	2390	0.08	2938	0.996	0.997	90.4016	0.074
1.038-1.088	0.08	256	0.083	2306	0.082	2816	0.996	0.996	90.9801	0.082
1.088-1.147	0.1	239	0.082	2152	0.084	2674	0.995	0.996	89.4166	0.086
1.147-1.216	0.09	220	0.086	1976	0.086	2527	0.996	0.996	86.9015	0.097
1.216-1.3	0.096	223	0.092	2012	0.092	2400	0.995	0.996	93.125	0.106
1.3-1.403	0.099	204	0.093	1834	0.093	2227	0.995	0.995	91.5132	0.113
1.403-1.537	0.101	182	0.108	1640	0.107	2017	0.994	0.994	90.3322	0.14
1.537-1.717	0.13	158	0.127	1421	0.127	1854	0.991	0.991	85.1672	0.17
1.717-1.98	0.153	155	0.151	1396	0.151	1629	0.986	0.987	95.2118	0.211
1.98-2.419	0.177	128	0.163	1146	0.164	1377	0.984	0.985	92.52	0.234
2.419-3.396	0.226	93	0.189	845	0.193	1083	0.971	0.977	86.6113	0.292
3.396-20.001	0.16	59	0.206	532	0.202	597	0.983	0.975	98.995	0.348

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