PDB-6c4z: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

ID or keywords:

Entry

Database: PDB / ID: 6c4z

Title

Cross-alpha Amyloid-like Structure alphaAmG - low resolution

Components

Cross-alpha Amyloid-like Structure alphaAmG - low resolution

Keywords

DE NOVO PROTEIN / Protein Design / Cross-alpha Amyloid

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.3 Å

Authors

Liu, L. / Zhang, S.Q.

Funding support

United States, 1items

Citation

Journal: Nat. Chem. Biol. / Year: 2018
Title: Designed peptides that assemble into cross-alpha amyloid-like structures.
Authors: Zhang, S.Q. / Huang, H. / Yang, J. / Kratochvil, H.T. / Lolicato, M. / Liu, Y. / Shu, X. / Liu, L. / DeGrado, W.F.

History

Deposition	Jan 13, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Nov 20, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6c4z.cif.gz	183.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6c4z.ent.gz	155.3 KB	Display	PDB format
PDBx/mmJSON format	6c4z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6c4z_validation.pdf.gz	477.6 KB	Display	wwPDB validaton report
Full document	6c4z_full_validation.pdf.gz	478.7 KB	Display
Data in XML	6c4z_validation.xml.gz	15.3 KB	Display
Data in CIF	6c4z_validation.cif.gz	21.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c4/6c4z ftp://data.pdbj.org/pub/pdb/validation_reports/c4/6c4z	HTTPS FTP

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Related structure data

Related structure data	6c4xC 6c4yC 6c50C 6c51C 6c52C 6d02C 6o3nC C: citing same article (ref.)
Similar structure data	6c4y-d 5d4v-2 3n4r-d 3qph-d 1zxe-1 5d4v-1 5uwv-2 4azs-d 5o02-d 4pvz-1 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: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

B: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

C: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

D: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

P: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

O: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

R: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

Q: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

E: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

F: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

G: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

H: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

L: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

K: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

N: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

M: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

J: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

I: Cross-alpha Amyloid-like Structure alphaAmG - low resolution

52.5 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: Fibrils confirmed byCryo_EM

Unit cell

Length a, b, c (Å)	172.279, 172.279, 153.758
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein/peptide	Cross-alpha Amyloid-like Structure alphaAmG - low resolution Mass: 2918.543 Da / Num. of mol.: 18 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O
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: 6.27 Å³/Da / Density % sol: 80.38 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 40% MDP, 0.2 M K/Na tartrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 8, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 3.3→172 Å / Num. obs: 38224 / % possible obs: 99.7 % / Redundancy: 16.8 % / Net I/σ(I): 15
Reflection shell	Resolution: 3.3→3.42 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Resolution: 3.3→149.2 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.913 / SU B: 49.364 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R: 0.671 / ESU R Free: 0.394 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27669	1042	5 %	RANDOM
R_work	0.24953	-	-	-
obs	0.25081	19794	99.74 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 89.195 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.59 Å²	-2.29 Å²	-0 Å²
2-	-	-4.59 Å²	0 Å²
3-	-	-	14.87 Å²

Refinement step

Cycle: 1 / Resolution: 3.3→149.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3562	0	0	1	3563

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	3598
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3858
X-RAY DIFFRACTION	r_angle_refined_deg	0.868	2.042	4812
X-RAY DIFFRACTION	r_angle_other_deg	0.756	3	8883
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.92	5	432
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	45.447	24.138	116
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.446	15	776
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.79	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.034	0.2	576
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3648
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	640
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	0.439	6.764	1800
X-RAY DIFFRACTION	r_mcbond_other	0.44	6.761	1798
X-RAY DIFFRACTION	r_mcangle_it	0.785	10.145	2232
X-RAY DIFFRACTION	r_mcangle_other	0.785	10.144	2231
X-RAY DIFFRACTION	r_scbond_it	0.376	6.83	1798
X-RAY DIFFRACTION	r_scbond_other	0.376	6.831	1799
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.703	10.226	2581
X-RAY DIFFRACTION	r_long_range_B_refined	2.225		12927
X-RAY DIFFRACTION	r_long_range_B_other	2.225		12923
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.295→3.381 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	74	-
R_work	0.35	1391	-
obs	-	-	97.73 %

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	2.2581	-1.1049	1.7151	2.9748	-4.6297	10.266	-0.3452	-0.0679	0.2885	0.2919	-0.076	-0.023	-0.3831	-1.0256	0.4212	0.0706	-0.0155	-0.008	0.4381	-0.1455	0.1365	-59.734	40.2837	-12.0103
2	2.3619	-0.6369	-0.078	2.308	-1.536	5.7228	-0.2925	0.2436	-0.1679	0.0351	-0.7354	-0.8791	0.5519	1.4672	1.0279	0.093	0.094	0.0783	0.4461	0.3468	0.4392	-51.4334	35.4781	-13.6626
3	1.7934	1.1491	-1.7472	2.2036	0.7463	4.4076	0.4286	0.0458	0.1273	0.3729	-0.6923	0.1906	-0.5793	-1.4028	0.2637	0.4453	0.3192	-0.2341	0.9315	-0.3281	0.2343	-53.9263	47.0811	-6.6838
4	1.5016	-1.2137	1.9996	2.335	-2.2591	6.0512	-0.0403	0.1163	0.0726	-0.2584	-0.3143	-0.6114	0.7512	0.3674	0.3547	0.2432	0.0155	0.0967	0.1499	0.1061	0.2505	-46.0157	42.7425	-10.6042
5	1.4524	-1.571	-1.9511	3.2166	4.5149	7.3932	0.0579	-0.072	-0.0187	-0.372	-0.2107	0.3754	-0.7377	-0.248	0.1529	0.2091	-0.0591	-0	0.1684	-0.1076	0.283	-15.0348	91.0636	-13.1672
6	2.0015	-1.1091	-1.7164	1.7	1.5826	6.7542	-0.2598	-0.5062	-0.0614	0.2081	-0.0126	0.1005	0.0881	1.0005	0.2724	0.1943	-0.0354	0.0468	0.3508	-0.0259	0.1358	-7.507	86.7962	-8.4597
7	0.6584	0.4704	-1.0149	2.8556	3.0275	7.566	-0.0827	-0.0135	0.1756	-0.2664	-0.4258	0.6743	-0.3943	-0.6677	0.5085	0.2257	-0.0168	-0.0473	0.1745	-0.0699	0.22	-10.828	100.0461	-11.6372
8	1.9119	-0.111	0.5432	1.6682	-0.11	8.1113	-0.3236	-0.0612	-0.1694	0.1744	-0.2245	0.0952	0.7388	0.6854	0.5481	0.2775	-0.0109	0.0587	0.1657	0.0323	0.1322	-2.0067	95.5124	-10.6307
9	5.8986	-2.5791	4.2182	2.8286	-1.5165	6.006	-0.3546	-0.7469	0.3148	0.413	0.186	-0.1031	-0.4156	-0.584	0.1686	0.1934	-0.0544	-0.0001	0.1829	0.0087	0.1636	-47.3671	55.4958	-4.7995
10	3.2786	-3.6134	2.4964	8.2375	-4.7351	5.7591	0.2908	0.1411	-0.0765	-0.3915	-0.2411	-0.211	0.262	0.1882	-0.0497	0.1314	-0.09	-0.0184	0.1126	0.009	0.1379	-41.9883	51.7279	-11.9134
11	6.7841	-2.3211	3.2641	3.3847	-2.4127	3.1765	-0.2264	-1.1313	0.2798	0.5074	0.2222	-0.1172	-0.261	-0.2423	0.0042	0.2507	-0.0613	0.0095	0.3054	-0.0552	0.1671	-38.0775	60.0091	-1.2098
12	5.7433	-5.3003	2.3282	6.5955	-2.4567	3.01	0.308	0.2397	0.0177	-0.3969	-0.2941	-0.2068	0.2427	0.1086	-0.0139	0.1468	-0.0993	0.0122	0.1291	0.0016	0.1804	-35.2118	58.5771	-10.5751
13	6.8236	-5.4337	-3.3331	9.936	4.9881	3.8442	0.3161	0.1683	0.0212	-0.4107	-0.2603	0.2656	-0.2128	-0.1206	-0.0558	0.1233	-0.0831	0.0182	0.1071	-0.0001	0.1125	-24.9854	75.2058	-11.3852
14	8.3029	-4.3365	-2.6932	4.3731	-0.4379	2.5872	-0.0859	-0.6253	-0.4227	0.3143	0.042	0.2951	-0.1338	0.3688	0.0439	0.2084	-0.1166	-0.015	0.2135	-0.0327	0.1509	-21.7515	72.6414	-2.6205
15	1.9517	-2.9179	-1.9555	5.1888	3.7423	3.0258	0.0657	0.0429	-0.1616	-0.3678	-0.3369	0.5514	-0.4937	-0.2934	0.2711	0.2668	-0.0181	0.013	0.2147	-0.1147	0.2829	-21.4299	84.4641	-10.3589
16	3.7198	-2.7106	-5.1037	3.9947	3.899	7.9693	-0.2554	-0.6414	-0.1931	0.4494	0.1518	0.2011	0.3066	0.5887	0.1036	0.2206	-0.0677	0.047	0.3025	0.0141	0.1521	-15.1869	80.972	-3.7499
17	2.7532	1.1644	1.6473	4.9157	-2.7268	3.7319	0.3583	0.1879	0.2333	-0.765	-0.5017	0.2591	0.695	0.5146	0.1434	0.7284	0.2108	-0.0941	0.2417	-0.1626	0.3281	-31.8596	68.39	-10.6147
18	11.2885	-5.6404	-0.0884	4.4649	0.5667	1.7373	-0.2655	-0.8805	-0.245	0.5107	0.209	0.1475	0.0273	0.042	0.0565	0.247	-0.1311	0.0146	0.183	0.0097	0.1834	-31.4224	68.3198	-1.0542

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 26
2	X-RAY DIFFRACTION	2	B	1 - 26
3	X-RAY DIFFRACTION	3	C	1 - 26
4	X-RAY DIFFRACTION	4	D	1 - 26
5	X-RAY DIFFRACTION	5	P	1 - 26
6	X-RAY DIFFRACTION	6	O	1 - 26
7	X-RAY DIFFRACTION	7	R	1 - 26
8	X-RAY DIFFRACTION	8	Q	1 - 26
9	X-RAY DIFFRACTION	9	E	1 - 26
10	X-RAY DIFFRACTION	10	F	1 - 26
11	X-RAY DIFFRACTION	11	G	1 - 26
12	X-RAY DIFFRACTION	12	H	1 - 26
13	X-RAY DIFFRACTION	13	L	1 - 26
14	X-RAY DIFFRACTION	14	K	1 - 26
15	X-RAY DIFFRACTION	15	N	1 - 26
16	X-RAY DIFFRACTION	16	M	1 - 26
17	X-RAY DIFFRACTION	17	J	1 - 26
18	X-RAY DIFFRACTION	18	I	1 - 26

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