PDB-6ug6: C3 symmetric peptide design number 1, Sporty, crystal form 2

ID or keywords:

Entry

Database: PDB / ID: 6ug6

Title

C3 symmetric peptide design number 1, Sporty, crystal form 2

Components

C3-1, Sporty, crystal form 2

Keywords

DE NOVO PROTEIN / cyclic peptide / 3-fold symmetric / L and D-amino acids

Function / homology

PHOSPHATE ION

Function and homology information

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 25, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 2, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 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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Download

PDBx/mmCIF format	6ug6.cif.gz	62.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6ug6.ent.gz	49.6 KB	Display	PDB format
PDBx/mmJSON format	6ug6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ug6_validation.pdf.gz	459.9 KB	Display	wwPDB validaton report
Full document	6ug6_full_validation.pdf.gz	460.7 KB	Display
Data in XML	6ug6_validation.xml.gz	5.2 KB	Display
Data in CIF	6ug6_validation.cif.gz	6.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ug/6ug6 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ug6	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 6ugbC 6ugcC C: citing same article (ref.)
Similar structure data	6bzm-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) 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: C3-1, Sporty, crystal form 2

B: C3-1, Sporty, crystal form 2

C: C3-1, Sporty, crystal form 2

D: C3-1, Sporty, crystal form 2

hetero molecules

7.33 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: C3-1, Sporty, crystal form 2

hetero molecules

defined by author&software
1.56 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: C3-1, Sporty, crystal form 2

hetero molecules

defined by author&software
1.85 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: C3-1, Sporty, crystal form 2

hetero molecules

defined by author&software
1.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: C3-1, Sporty, crystal form 2

hetero molecules

defined by author&software
2.11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	28.530, 29.960, 30.100
Angle α, β, γ (deg.)	109.499, 108.863, 107.911
Int Tables number	2
Space group name H-M	P-1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains A B
2	1	Chains A C
3	1	Chains A D
4	1	Chains B C
5	1	Chains B D
6	1	Chains C D

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide	C3-1, Sporty, crystal form 2 Mass: 1423.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ab initio design / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 58 molecules

#2: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 1.78 Å³/Da / Density % sol: 31.02 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.09 M sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09 M ammonium sulfate, 0.1 M HEPES, 0.1M MOPS pH 7.5, 12.5% v/v MPD, 12.5% PEG 1000, 12.5% PEG 3350

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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→24.992 Å / Num. obs: 28588 / % possible obs: 88.9 % / Redundancy: 3.511 % / B_iso Wilson estimate: 9.781 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.052 / R_rim(I) all: 0.062 / Χ²: 1.156 / Net I/σ(I): 6.92

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	3.122	0.156	3.58	1633	0.992	0.19	68.4
1.13-1.16	3.404	0.162	4	1919	0.989	0.194	82.9
1.16-1.19	3.455	0.141	4.38	2007	0.993	0.168	87.9
1.19-1.23	3.381	0.123	4.72	1906	0.993	0.147	88.2
1.23-1.27	3.532	0.123	4.86	1877	0.994	0.146	89.3
1.27-1.31	3.305	0.121	4.78	1898	0.992	0.145	90.6
1.31-1.36	3.515	0.111	5.29	1784	0.993	0.132	90.5
1.36-1.42	3.676	0.102	5.99	1727	0.994	0.119	91.9
1.42-1.48	3.608	0.089	6.36	1680	0.996	0.105	91.5
1.48-1.56	3.609	0.078	7.07	1592	0.996	0.093	92.1
1.56-1.64	3.601	0.071	7.42	1531	0.996	0.083	90.8
1.64-1.74	3.391	0.062	8.02	1411	0.997	0.074	90.7
1.74-1.86	3.554	0.053	8.62	1343	0.998	0.062	91.5
1.86-2.01	3.76	0.048	9.53	1306	0.998	0.056	93.4
2.01-2.2	3.697	0.043	10.85	1176	0.997	0.051	93.6
2.2-2.46	3.681	0.038	11.12	1065	0.998	0.045	93.8
2.46-2.84	3.644	0.038	12.35	956	0.999	0.045	93.7
2.84-3.48	3.332	0.035	12.4	784	0.998	0.042	92
3.48-4.92	3.747	0.031	13.73	647	0.999	0.036	96.6
4.92-24.992	3.656	0.033	14.43	346	0.998	0.04	95.8

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Processing

Software

Name	Version	Classification
XDS	20190315	data reduction
XSCALE	20190315	data scaling
REFMAC	5.8.0253	refinement
PDB_EXTRACT	3.25	data extraction
SHELXD		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.1→24.992 Å / Cor.coef. F_o:F_c: 0.984 / Cor.coef. F_o:F_c free: 0.973 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2137	2859	10.001 %
R_work	0.1801	-	-
all	0.183	-	-
obs	-	28587	89.393 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 8.572 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.069 Å²	-0.348 Å²	0.024 Å²
2-	-	-0.309 Å²	0.049 Å²
3-	-	-	0.267 Å²

Refinement step

Cycle: LAST / Resolution: 1.1→24.992 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	396	0	105	42	543

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	547
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	597
X-RAY DIFFRACTION	r_angle_refined_deg	1.685	1.803	760
X-RAY DIFFRACTION	r_angle_other_deg	0.543	1.604	1335
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.643	5	52
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.413	17.368	38
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.25	15	50
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.919	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	65
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	474
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	98
X-RAY DIFFRACTION	r_nbd_refined	0.289	0.2	58
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	427
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	216
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	307
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	23
X-RAY DIFFRACTION	r_metal_ion_refined	0.407	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.153	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.11	0.2	133
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.15	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	0.511	0.42	196
X-RAY DIFFRACTION	r_mcbond_other	0.504	0.42	195
X-RAY DIFFRACTION	r_mcangle_it	0.586	0.642	246
X-RAY DIFFRACTION	r_mcangle_other	0.585	0.641	247
X-RAY DIFFRACTION	r_scbond_it	2.002	0.889	351
X-RAY DIFFRACTION	r_scbond_other	1.999	0.891	352
X-RAY DIFFRACTION	r_scangle_it	2.875	1.319	512
X-RAY DIFFRACTION	r_scangle_other	2.872	1.321	513
X-RAY DIFFRACTION	r_lrange_it	1.892	6.493	439
X-RAY DIFFRACTION	r_lrange_other	1.75	6.372	436
X-RAY DIFFRACTION	r_rigid_bond_restr	1.218	3	1144
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.142	0.05	347
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.189	0.05	337
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.141	0.05	347
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.165	0.05	305
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.005	0.05	325
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.175	0.05	334

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
1.1-1.129	0.246	164	0.241	1469	0.242	2379	0.976	0.98	68.6423	0.219
1.129-1.159	0.24	191	0.212	1718	0.214	2285	0.976	0.981	83.5449	0.196
1.159-1.193	0.241	200	0.186	1804	0.191	2277	0.975	0.986	88.0105	0.176
1.193-1.23	0.213	191	0.185	1718	0.188	2160	0.979	0.986	88.3796	0.177
1.23-1.27	0.188	187	0.186	1680	0.186	2078	0.986	0.986	89.846	0.178
1.27-1.314	0.221	189	0.191	1703	0.194	2075	0.976	0.983	91.1807	0.18
1.314-1.364	0.216	179	0.173	1609	0.177	1969	0.98	0.987	90.8075	0.166
1.364-1.419	0.189	171	0.159	1539	0.162	1860	0.986	0.989	91.9355	0.156
1.419-1.482	0.214	169	0.152	1521	0.157	1832	0.979	0.99	92.2489	0.158
1.482-1.554	0.17	158	0.147	1428	0.15	1718	0.986	0.991	92.3166	0.154
1.554-1.638	0.185	152	0.147	1371	0.15	1663	0.987	0.99	91.5815	0.159
1.638-1.737	0.179	142	0.159	1271	0.161	1549	0.985	0.988	91.2201	0.178
1.737-1.856	0.224	135	0.172	1221	0.177	1476	0.98	0.987	91.8699	0.202
1.856-2.004	0.16	129	0.15	1162	0.151	1372	0.991	0.991	94.0962	0.195
2.004-2.194	0.171	119	0.154	1066	0.156	1257	0.987	0.99	94.2721	0.209
2.194-2.45	0.182	106	0.173	957	0.173	1124	0.984	0.988	94.573	0.25
2.45-2.825	0.213	96	0.188	858	0.191	1010	0.972	0.986	94.4554	0.27
2.825-3.449	0.221	79	0.196	719	0.198	858	0.975	0.983	93.007	0.314
3.449-4.831	0.314	65	0.207	579	0.217	656	0.961	0.983	98.1707	0.384
4.831-24.992	0.351	37	0.274	331	0.28	375	0.967	0.979	98.1333	0.61

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