PDB-6uf9: S4 symmetric peptide design number 1, Tim apo form

ID or keywords:

Entry

Database: PDB / ID: 6uf9

Title

S4 symmetric peptide design number 1, Tim apo form

Components

S4-1, Tim apo-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: 1.1 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	6uf9.cif.gz	26.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6uf9.ent.gz	17 KB	Display	PDB format
PDBx/mmJSON format	6uf9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6uf9_validation.pdf.gz	431.6 KB	Display	wwPDB validaton report
Full document	6uf9_full_validation.pdf.gz	431.6 KB	Display
Data in XML	6uf9_validation.xml.gz	3.1 KB	Display
Data in CIF	6uf9_validation.cif.gz	3.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uf/6uf9 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/6uf9	HTTPS FTP

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Related structure data

Related structure data	6ucxC 6ud9C 6udrC 6udwC 6udzC 6uf4C 6uf7C 6uf8C 6ufaC 6ufuC 6ug2C 6ug3C 6ug6C 6ugbC 6ugcC C: citing same article (ref.)
Similar structure data	1go6-3 1gac-d 5kx0-d 5kwo-d 6ufa-d 2lix-d 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: S4-1, Tim apo-form

hetero molecules

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

1

A: S4-1, Tim apo-form

hetero molecules

A: S4-1, Tim apo-form

hetero molecules

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

Unit cell

Length a, b, c (Å)	27.770, 28.350, 12.220
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein/peptide	S4-1, Tim apo-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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H₂O
Compound details	The asymmetric unit contains half of the molecule. The second half is generated by a ...The asymmetric unit contains half of the molecule. The second half is generated by a crystallographic symmetry operator.
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: 1.64 Å³/Da / Density % sol: 25.2 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 3.15 M ammonium sulfate, 0.1 M citric acid, pH 5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER X 16M / 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: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.1→19.838 Å / Num. obs: 4233 / % possible obs: 99.7 % / Redundancy: 10.311 % / B_iso Wilson estimate: 15.47 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.094 / R_rim(I) all: 0.099 / Χ²: 0.881 / Net I/σ(I): 13.01

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
1.1-1.13	7.19	0.511	3.83	300	0.912	0.551	98.4
1.13-1.16	9.266	0.394	5.53	286	0.957	0.418	99.3
1.16-1.19	9.324	0.365	5.95	290	0.965	0.386	99
1.19-1.23	9.443	0.304	6.96	287	0.983	0.322	99
1.23-1.27	10	0.326	7.01	257	0.976	0.344	100
1.27-1.31	9.603	0.217	8.73	267	0.995	0.23	100
1.31-1.36	10.241	0.209	10.58	266	0.983	0.22	100
1.36-1.42	11.074	0.178	11.77	243	0.993	0.187	100
1.42-1.48	10.907	0.159	13.15	237	0.99	0.167	100
1.48-1.56	10.807	0.151	14.21	228	0.987	0.159	100
1.56-1.64	11.382	0.128	15.91	217	0.993	0.134	100
1.64-1.74	10.648	0.11	17.55	216	0.998	0.116	100
1.74-1.86	11.287	0.102	18.78	195	0.994	0.107	100
1.86-2.01	12.275	0.089	22.05	189	0.997	0.093	100
2.01-2.2	11.942	0.089	22.83	171	0.997	0.093	100
2.2-2.46	11.799	0.08	23.46	159	0.998	0.083	100
2.46-2.84	11.399	0.074	23.07	138	0.996	0.078	100
2.84-3.48	10.439	0.078	22.39	123	0.997	0.082	100
3.48-4.92	11.687	0.081	24.46	99	0.993	0.085	100
4.92-19.838	9.308	0.116	21.37	65	0.992	0.124	100

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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
SHELXD		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.1→19.838 Å / Cor.coef. F_o:F_c: 0.987 / Cor.coef. F_o:F_c free: 0.979 / WR_factor R_free: 0.188 / WR_factor R_work: 0.144 / SU B: 1.347 / SU ML: 0.028 / Average fsc free: 0.9447 / Average fsc work: 0.9624 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1734	424	10.017 %
R_work	0.128	3809	-
all	0.132	-	-
obs	-	4233	99.647 %

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: 16.929 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.214 Å²	0 Å²	0 Å²
2-	-	-0.021 Å²	0 Å²
3-	-	-	-0.193 Å²

Refinement step

Cycle: LAST / Resolution: 1.1→19.838 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	102	0	10	17	129

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	146
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	150
X-RAY DIFFRACTION	r_angle_refined_deg	1.994	1.659	201
X-RAY DIFFRACTION	r_angle_other_deg	0.767	1.606	355
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.809	5	19
X-RAY DIFFRACTION	r_dihedral_angle_other_1_deg	1.713	10	1
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.051	27.5	4
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	3.789	10	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.887	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.152	0.2	15
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	156
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	24
X-RAY DIFFRACTION	r_nbd_refined	0.254	0.2	32
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.254	0.2	108
X-RAY DIFFRACTION	r_nbtor_refined	0.207	0.2	56
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.136	0.2	55
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	17
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.007	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.62	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.314	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	1.363	1.039	57
X-RAY DIFFRACTION	r_mcbond_other	1.361	1.038	57
X-RAY DIFFRACTION	r_mcangle_it	1.809	1.57	70
X-RAY DIFFRACTION	r_mcangle_other	1.798	1.567	71
X-RAY DIFFRACTION	r_scbond_it	4.291	1.717	89
X-RAY DIFFRACTION	r_scbond_other	4.035	1.622	82
X-RAY DIFFRACTION	r_scangle_it	5.627	2.419	126
X-RAY DIFFRACTION	r_scangle_other	5.062	2.202	115
X-RAY DIFFRACTION	r_lrange_it	6.851	20.456	148
X-RAY DIFFRACTION	r_lrange_other	5.026	17.611	140
X-RAY DIFFRACTION	r_rigid_bond_restr	4.235	3	296

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
1.1-1.128	0.321	30	0.247	269	0.253	306	0.818	0.897	97.7124	0.222
1.128-1.159	0.235	29	0.197	254	0.201	285	0.918	0.934	99.2982	0.171
1.159-1.193	0.283	29	0.188	262	0.197	294	0.917	0.936	98.9796	0.168
1.193-1.229	0.267	28	0.184	254	0.193	285	0.946	0.944	98.9474	0.163
1.229-1.269	0.217	26	0.17	232	0.175	258	0.928	0.945	100	0.151
1.269-1.314	0.206	26	0.147	239	0.153	265	0.955	0.964	100	0.137
1.314-1.363	0.234	27	0.141	242	0.149	269	0.948	0.97	100	0.129
1.363-1.419	0.186	24	0.116	215	0.121	239	0.959	0.98	100	0.11
1.419-1.481	0.232	24	0.111	219	0.121	243	0.956	0.98	100	0.109
1.481-1.553	0.184	23	0.122	209	0.129	232	0.961	0.978	100	0.12
1.553-1.637	0.112	21	0.11	188	0.111	209	0.972	0.979	100	0.114
1.637-1.735	0.179	22	0.116	198	0.122	220	0.967	0.982	100	0.127
1.735-1.854	0.139	19	0.129	172	0.13	191	0.973	0.977	100	0.146
1.854-2.001	0.185	19	0.121	168	0.128	187	0.965	0.978	100	0.145
2.001-2.19	0.197	17	0.127	155	0.133	172	0.956	0.981	100	0.155
2.19-2.445	0.131	17	0.105	147	0.108	164	0.984	0.985	100	0.121
2.445-2.816	0.189	13	0.116	123	0.123	136	0.974	0.984	100	0.162
2.816-3.431	0.128	12	0.124	108	0.124	120	0.985	0.984	100	0.184
3.431-4.782	0.156	11	0.106	92	0.111	103	0.979	0.992	100	0.161
4.782-19.838	0.13	7	0.14	62	0.139	69	0.989	0.984	100	0.233

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