PDB-8kck: De novo design protein -N9

ID or keywords:

Entry

Database: PDB / ID: 8kck

Title

De novo design protein -N9

Components

De novo design protein -N9

Keywords

DE NOVO PROTEIN / De novo design protein

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Wang, S. / Liu, Y.

Funding support

1items

Citation

Journal: Nat.Methods / Year: 2024
Title: De novo protein design with a denoising diffusion network independent of pretrained structure prediction models.
Authors: Liu, Y. / Wang, S. / Dong, J. / Chen, L. / Wang, X. / Wang, L. / Li, F. / Wang, C. / Zhang, J. / Wang, Y. / Wei, S. / Chen, Q. / Liu, H.

History

Deposition	Aug 7, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2025	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8kck.cif.gz	94.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8kck.ent.gz	71.3 KB	Display	PDB format
PDBx/mmJSON format	8kck.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8kck_validation.pdf.gz	416.4 KB	Display	wwPDB validaton report
Full document	8kck_full_validation.pdf.gz	417.8 KB	Display
Data in XML	8kck_validation.xml.gz	12.7 KB	Display
Data in CIF	8kck_validation.cif.gz	17.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kc/8kck ftp://data.pdbj.org/pub/pdb/validation_reports/kc/8kck	HTTPS FTP

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Related structure data

Related structure data	8k7mC 8k7oC 8k7zC 8k83C 8k84C 8k8fC 8k8gC 8k8iC 8ka6C 8ka7C 8kacC 8kc0C 8kc1C 8kc4C 8kc5C 8kc8C 8kcjC 8kdqC 8w97C 8wwcC 8wx8C 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: De novo design protein -N9

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

1

A: De novo design protein -N9

defined by author&software
Evidence: gel filtration
42.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	35.011, 75.997, 129.640
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-314- HOH
2	1	A-375- HOH
3	1	A-415- HOH
4	1	A-423- HOH

#1: Protein	De novo design protein -N9 Mass: 21146.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.32 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion Details: 0.2Msodium chloride 0.1M MES pH6.0 20% w/v PEG2000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.35→43.21 Å / Num. obs: 38488 / % possible obs: 100 % / Redundancy: 9 % / B_iso Wilson estimate: 15.47 Å² / CC_1/2: 1 / Net I/σ(I): 23.22
Reflection shell	Resolution: 1.35→1.37 Å / Num. unique obs: 1939 / CC_1/2: 0.839

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.35→25.61 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2153	1939	5.04 %
R_work	0.1836	-	-
obs	0.1852	38477	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.35→25.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1406	0	0	208	1614

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	1429
X-RAY DIFFRACTION	f_angle_d	1.336	1959
X-RAY DIFFRACTION	f_dihedral_angle_d	5.071	222
X-RAY DIFFRACTION	f_chiral_restr	0.103	249
X-RAY DIFFRACTION	f_plane_restr	0.015	258

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.35-1.38	0.2786	128	0.2618	2549	X-RAY DIFFRACTION	100
1.38-1.42	0.2509	159	0.2371	2548	X-RAY DIFFRACTION	100
1.42-1.46	0.2548	141	0.2181	2585	X-RAY DIFFRACTION	100
1.46-1.51	0.2515	127	0.2042	2580	X-RAY DIFFRACTION	100
1.51-1.56	0.2489	131	0.1998	2582	X-RAY DIFFRACTION	100
1.56-1.63	0.2304	124	0.1989	2599	X-RAY DIFFRACTION	100
1.63-1.7	0.2308	142	0.1928	2586	X-RAY DIFFRACTION	100
1.7-1.79	0.211	133	0.1832	2592	X-RAY DIFFRACTION	100
1.79-1.9	0.1959	126	0.1842	2646	X-RAY DIFFRACTION	100
1.9-2.05	0.2144	125	0.1815	2597	X-RAY DIFFRACTION	100
2.05-2.26	0.1855	160	0.1602	2601	X-RAY DIFFRACTION	100
2.26-2.58	0.2096	149	0.1771	2638	X-RAY DIFFRACTION	100
2.58-3.25	0.2159	151	0.1781	2653	X-RAY DIFFRACTION	100
3.25-25.61	0.216	143	0.1807	2782	X-RAY DIFFRACTION	100

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	4.2755	3.8982	1.2975	5.6386	0.0464	1.2304	0.3364	0.1179	-0.3797	0.044	-0.0895	0.0572	0.3679	0.2109	-0.1154	0.183	0.1241	-0.0515	0.1725	-0.0747	0.1519	6.4754	-12.8695	19.6264
2	7.0512	-1.8282	-6.8123	0.6114	1.0928	6.1924	0.2905	-0.3057	-0.1314	-0.0799	-0.1569	0.0773	-0.2605	0.3209	-0.152	0.1077	0.0036	-0.0029	0.1636	-0.0255	0.0886	2.8605	-0.233	27.3726
3	3.536	-1.0631	0.3294	8.974	-7.3578	6.5392	0.1519	-0.0978	-0.0006	0.3641	0.0944	0.6087	-0.5829	0.1597	-0.2842	0.2053	0.0384	0.0166	0.1193	-0.0259	0.2657	-10.6857	11.1512	25.723
4	4.0504	0.5437	1.7871	1.7077	-2.1179	4.6873	-0.0408	0.1716	0.2	-0.329	0.2049	-0.497	0.2333	-0.0808	-0.0578	0.2298	0.0015	-0.0213	0.2814	-0.0476	0.1979	-9.9617	-3.1249	7.6613
5	1.333	0.4413	-0.3498	8.6032	-3.3306	5.5839	0.0599	0.1449	-0.0201	-0.0104	0.0894	-0.1676	0.1898	0.2207	-0.1441	0.1308	0.0212	-0.0157	0.1761	-0.0601	0.0876	-1.4019	-1.5028	5.1978
6	2.8047	-0.1074	1.118	2.8636	-0.0552	4.6878	0.0041	0.2097	-0.0741	-0.192	0.0849	-0.3731	-0.0427	0.0946	-0.1025	0.1202	0.0296	0.0037	0.1271	-0.0127	0.1411	-5.3207	1.2395	10.1615
7	8.6918	2.5969	-3.3016	2.955	-2.1251	3.9896	0.0467	-0.0857	-0.0294	0.0244	0.0307	-0.1023	-0.0633	0.1468	0.0002	0.1043	0.0197	-0.022	0.1058	-0.025	0.0879	-0.438	0.9814	20.4579
8	7.9435	3.3387	-2.0685	5.173	-1.6456	3.7476	0.0983	0.0073	0.418	-0.0188	0.0927	0.1839	-0.2717	-0.072	-0.3135	0.1085	0.0397	-0.0004	0.0876	-0.0036	0.1188	-8.2471	6.0132	20.8879
9	2.9725	0.4376	-0.3597	2.7287	-1.0963	1.7917	0.0286	0.1965	-0.1726	-0.1015	0.062	0.0633	0.1849	0.2646	-0.0627	0.1062	0.0328	-0.0394	0.1357	-0.0555	0.0788	0.6714	-4.214	15.1739
10	7.3333	2.1722	-6.5742	1.1455	-1.7537	7.4437	0.1863	0.2824	0.3755	0.0493	0.1072	0.0737	0.0579	-0.0877	-0.1573	0.1079	0.011	-0.0131	0.1386	-0.0162	0.1035	1.6896	-0.611	23.5434
11	8.1661	-0.1892	-3.728	1.6631	0.9103	3.455	-0.1008	-0.1575	-0.2631	0.2081	0.1013	-0.1895	0.3368	0.1943	-0.0481	0.3126	0.0252	-0.1111	0.1066	-0.0114	0.1319	0.8103	-11.1738	28.3728

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 31 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 44 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 45 through 61 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 62 through 79 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 80 through 114 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 115 through 125 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 126 through 141 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 142 through 171 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 172 through 188 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 189 through 207 )

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