PDB-8kc5: De novo design protein -T09

ID or keywords:

Entry

Database: PDB / ID: 8kc5

Title

De novo design protein -T09

Components

De novo design protein -T09

Keywords

DE NOVO PROTEIN / De novo design protein

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 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 6, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Aug 7, 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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Download

PDBx/mmCIF format	8kc5.cif.gz	217.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8kc5.ent.gz	145.7 KB	Display	PDB format
PDBx/mmJSON format	8kc5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kc/8kc5 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/8kc5	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 8kc8C 8kcjC 8kckC 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 -T09

B: De novo design protein -T09

52.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: De novo design protein -T09

defined by author
Evidence: gel filtration
26.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: De novo design protein -T09

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

Unit cell

Length a, b, c (Å)	46.026, 59.415, 85.421
Angle α, β, γ (deg.)	90.000, 94.830, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	De novo design protein -T09 Mass: 26250.498 Da / Num. of mol.: 2 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.: 68 / 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: 2.22 Å³/Da / Density % sol: 44.51 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / Details: 0.2M Imidazole malate pH5.5 33% w/v PEG600

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.3→48.72 Å / Num. obs: 20207 / % possible obs: 97.92 % / Redundancy: 2 % / CC_1/2: 0.999 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 5.5 % / Num. unique obs: 1944 / CC_1/2: 0.793

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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: 2.3→36.3 Å / SU ML: 0.3609 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2547	3863	9.91 %
R_work	0.2068	35105	-
obs	0.2116	20181	97.31 %

Solvent computation

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

Displacement parameters

B_iso mean: 60.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→36.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3298	0	0	68	3366

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	3318
X-RAY DIFFRACTION	f_angle_d	0.5059	4530
X-RAY DIFFRACTION	f_chiral_restr	0.0402	605
X-RAY DIFFRACTION	f_plane_restr	0.0041	571
X-RAY DIFFRACTION	f_dihedral_angle_d	4.5235	490

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 (%)
2.3-2.33	0.4049	124	0.3285	1239	X-RAY DIFFRACTION	96.87
2.33-2.36	0.4155	136	0.3336	1272	X-RAY DIFFRACTION	96.57
2.36-2.39	0.3856	152	0.3166	1215	X-RAY DIFFRACTION	97.16
2.39-2.42	0.335	122	0.2986	1303	X-RAY DIFFRACTION	97.2
2.42-2.46	0.3338	156	0.28	1186	X-RAY DIFFRACTION	96.13
2.46-2.49	0.3612	139	0.2772	1257	X-RAY DIFFRACTION	97.35
2.49-2.53	0.3346	129	0.2649	1266	X-RAY DIFFRACTION	97.35
2.53-2.57	0.3447	144	0.2751	1247	X-RAY DIFFRACTION	96.73
2.57-2.62	0.3396	154	0.274	1217	X-RAY DIFFRACTION	97.1
2.62-2.66	0.3134	136	0.2503	1271	X-RAY DIFFRACTION	96.77
2.67-2.72	0.3703	119	0.2482	1287	X-RAY DIFFRACTION	97.37
2.72-2.77	0.3674	131	0.2435	1222	X-RAY DIFFRACTION	97.62
2.77-2.83	0.3632	147	0.2358	1278	X-RAY DIFFRACTION	97.47
2.83-2.9	0.305	143	0.233	1250	X-RAY DIFFRACTION	98.17
2.9-2.97	0.2854	140	0.2154	1260	X-RAY DIFFRACTION	97.49
2.97-3.05	0.2476	136	0.2091	1268	X-RAY DIFFRACTION	97.43
3.05-3.14	0.2969	131	0.2211	1261	X-RAY DIFFRACTION	97.89
3.14-3.24	0.3044	142	0.2176	1266	X-RAY DIFFRACTION	98.12
3.24-3.36	0.2592	133	0.2018	1270	X-RAY DIFFRACTION	97.97
3.36-3.49	0.2226	141	0.1867	1244	X-RAY DIFFRACTION	98.3
3.49-3.65	0.2166	147	0.1961	1248	X-RAY DIFFRACTION	97.69
3.65-3.84	0.2472	137	0.1817	1262	X-RAY DIFFRACTION	97.22
3.84-4.08	0.1985	143	0.191	1256	X-RAY DIFFRACTION	97.76
4.08-4.4	0.2349	122	0.1638	1254	X-RAY DIFFRACTION	96.9
4.4-4.84	0.2115	128	0.167	1255	X-RAY DIFFRACTION	97.33
4.84-5.54	0.1943	142	0.1867	1279	X-RAY DIFFRACTION	97.87
5.54-6.96	0.2329	148	0.2249	1243	X-RAY DIFFRACTION	97.27
6.98-36.3	0.1925	141	0.1604	1229	X-RAY DIFFRACTION	95.6

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	6.03647270727	4.76501820823	1.22872186927	6.50251538623	0.419107393862	3.16263154819	0.576478241089	-0.298140697282	-0.536370070568	0.764457642507	-0.507866125843	-0.695739808928	0.180538660804	0.00523044326145	-0.115471413949	0.642373018779	0.00631038227446	-0.166467219163	0.353471860673	0.00617841360063	0.411488652788	-15.0381524598	-16.8995082809	10.6762045112
2	4.59495828357	4.70103870672	0.642492938164	8.33864836839	0.193077663647	3.95074474208	0.159600405416	-0.295003516262	0.309874454755	0.106199830426	-0.530455269469	0.436387401278	-0.286719017364	-0.394046775765	0.428647678241	0.461391369853	0.0648854043667	-0.0851862218875	0.305010050569	-0.0314508692587	0.331777532886	-23.4839926204	-19.736258759	8.35046042962
3	9.67965449482	1.45552442585	-3.36164905058	2.10327244236	4.56191510152	2.28166468608	0.477729072869	0.0780875289289	0.243803856369	-0.224762220836	-0.683682119396	0.966590486917	-1.0288821011	-0.6187849754	0.243676344539	0.742429961767	0.0782291005162	0.0145417922911	0.360212504473	-0.0106459619058	0.460636424294	-30.9159391803	-24.2533597438	2.9553617366
4	7.17774594808	4.92302790117	2.77858418868	7.23774387406	-2.83034329735	6.05490135807	-0.149568031951	0.546136022348	1.35438157653	-0.589009691529	0.169549797161	0.498445981166	0.876616097697	-0.696645153779	0.440667341988	0.798711801298	0.0987384156157	-0.0449679475457	0.327182633459	0.00389843837336	0.537231484599	-23.2660400912	-17.9360786261	-3.11465993643
5	9.81117725422	3.3275623579	-0.246938433272	8.29127952509	-0.224685391044	9.50879392224	-1.05593887544	0.624879091879	-0.222673749992	-1.66854237052	0.203709376888	2.46058328122	0.938017637501	-0.305997751493	0.502271161758	1.25311279923	-0.00261695547376	-0.445132170899	0.268488541324	-0.121184392424	0.835254175704	-27.8311050032	-21.9438993406	-10.1704337279
6	4.84598556148	-1.60807423114	-0.649361800879	6.21275975693	-1.42227693193	5.93548348067	0.170120137078	-0.464045371298	0.285380948004	1.09843724148	-0.334101827754	-0.417942492192	-0.457099406814	0.788879248503	0.218079494484	0.57911902563	-0.10166405617	-0.157650029879	0.330009259865	0.0335879859236	0.381033554632	7.32736065539	-12.7281090626	50.5328331894
7	5.2641537659	0.238582011617	-0.722504793298	5.40762645	-0.0671265694713	5.19367645527	0.0244538523598	0.623044893951	-0.21641776389	-0.339919084524	-0.495033561358	-1.23750112955	0.095877755629	1.53015186851	0.418174047343	0.351772793434	0.0514482243053	0.00987744389703	0.708619349229	0.101303119134	0.577470203993	16.1744372712	-20.9656397627	37.7580583444
8	6.00403216586	-2.96549701185	1.78666859957	2.24325849969	-2.35860298279	6.36403887142	-0.599136414561	0.347610518265	-0.137275738658	-0.945898787785	0.259910797065	-0.893984516028	0.222479699435	0.175514617192	0.413557728672	0.418641623972	-0.0380814970786	0.0415431514949	0.399569941707	-0.02158343868	0.314562736487	8.02031082616	-13.2420807858	31.3548501616
9	4.4226187386	-3.02556521649	0.810947366737	6.34690168051	-0.443185127332	5.03722164411	0.67145295183	0.870706842866	0.715003901284	-1.28790953184	-0.731024505343	-0.954445149094	-0.0239072358904	0.996498140358	0.0942654143538	0.566521368724	0.0588401822884	0.0851434023418	0.574439522082	0.171763414804	0.440420510319	6.13014906238	-10.4623613854	26.5931433182
10	4.92118374948	-2.17625889107	0.393056802632	2.74233853381	0.696467183927	9.04834199692	0.0890363068561	-0.0358026844488	0.184847583184	0.0890712945287	-0.311824385397	-0.437245140854	0.0403660699006	-0.0984997138047	0.222775500869	0.26002679239	0.00227944411262	-0.0277892899377	0.280828469215	-0.00241512613007	0.297412767728	-0.744320866631	-6.13016601908	29.4433600458
11	2.9197398843	-3.17560519945	0.498431067108	7.27068327213	0.494132650166	5.14911483713	0.0603521696707	-0.0414986534851	0.0688201584609	-0.00413813552234	-0.272975426754	0.270118802909	-0.401790781533	-0.232945253234	0.212755953643	0.307619027064	-0.0456167611293	0.0076523910582	0.284704764815	-0.0657823229041	0.284883500986	-6.92474168903	-4.00589071981	34.3376171071
12	2.76572896786	0.569046901377	6.73516432886	8.58775719111	1.74898082805	6.75328082956	0.612019565519	-0.583621561437	-0.66974951902	0.391212694495	-0.40019029161	0.1720438758	0.396271162315	-0.755830386317	-0.369093465388	0.458763745094	-0.00651053810627	0.0336412494312	0.357930720452	-0.0386669882146	0.39138393938	-12.1289030317	0.485650861185	42.0996540448
13	5.27863465726	-5.38208799538	1.1057842251	5.67302401729	-1.57681594468	9.19449273705	-0.0106930586926	-0.165234102098	0.561287492725	0.884214067896	-0.0845731638319	0.0969735659293	-0.239372929216	0.121084361015	0.00208479564916	0.668590323175	-0.0536560900376	0.0167106891794	0.242016405674	-0.0209358634995	0.463092465616	-3.41077552321	-3.51025888777	49.8835235636
14	6.12268165915	1.28801237786	1.60528803032	6.61483122327	0.185872522601	8.44031184689	-0.276870644893	1.03868231605	0.287075951474	-1.99490569459	-0.0476308454468	0.122906275503	0.698657187436	0.0348645131444	0.323784026741	1.22240062581	0.116579792728	-0.155602240528	0.454957252489	0.000905058486194	0.416001779364	-20.0718326609	-14.1605905138	-13.2764766429
15	6.09083111388	1.50272531545	1.24565258595	7.08878137972	-0.512886446728	5.0210834239	0.00149113500335	0.508193040166	-0.378631244633	-1.43531062506	-0.252978402921	-0.625911688181	0.228484788361	0.832408021066	0.344753716217	0.767153252785	0.149303494829	0.106985397068	0.42117199364	0.078032506869	0.453557239774	-9.9177371329	-6.51605102658	-9.33410884433
16	10.1926707484	-0.697506827553	3.98179808891	9.30105462488	-2.09567568805	2.6611357319	0.505606021597	-0.221989338447	0.474889820279	0.068357533589	-0.487576763018	-1.28800956281	0.377286354522	1.28938446494	0.0974708408917	0.564936644075	-0.0153628538533	0.0374865553646	0.606674088025	0.0317972095718	0.538092420363	-3.26374446128	-4.80705929958	2.31436082459
17	5.39518896578	0.856978796867	-1.30554753237	5.437992636	-1.47992130906	7.68179146071	0.367232520361	-0.922291684417	-0.654284200639	1.80634135678	-0.0792562127628	-0.83597770721	0.45222949136	0.160136994811	-0.146944200615	0.664083179964	0.0173807085594	-0.285704101918	0.521246302722	0.0790082798715	0.508842071933	-8.58820968139	-10.4682091621	7.36243815603
18	2.44962463135	-1.03074908772	1.49535068187	8.18922818003	-3.73238259013	2.1896030953	-0.0426786560108	0.271953760197	0.0394585361279	-1.29274709633	0.0355977841614	-1.13204653762	-0.584935288489	1.42774427121	-0.299673991423	0.886842126343	-0.100467734637	-0.214232402168	0.760085667904	-0.0847749901562	0.595016365715	-3.58063726868	-12.2555886473	15.3061484819

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 128 through 162 )	B	B	128 - 162	128 - 162
2	2	chain 'B' and (resid 163 through 189 )	B	B	163 - 189	163 - 189
3	3	chain 'B' and (resid 190 through 203 )	B	B	190 - 203	190 - 203
4	4	chain 'B' and (resid 204 through 217 )	B	B	204 - 217	204 - 216
5	5	chain 'B' and (resid 218 through 229 )	B	B	218 - 229	217 - 228
6	6	chain 'A' and (resid 1 through 65 )	A	A	1 - 65	1 - 65
7	7	chain 'A' and (resid 66 through 101 )	A	A	66 - 101	66 - 101
8	8	chain 'A' and (resid 102 through 115 )	A	A	102 - 115	102 - 115
9	9	chain 'A' and (resid 116 through 139 )	A	A	116 - 139	116 - 139
10	10	chain 'A' and (resid 140 through 162 )	A	A	140 - 162	140 - 162
11	11	chain 'A' and (resid 163 through 189 )	A	A	163 - 189	163 - 189
12	12	chain 'A' and (resid 190 through 203 )	A	A	190 - 203	190 - 203
13	13	chain 'A' and (resid 204 through 229 )	A	A	204 - 229	204 - 227
14	14	chain 'B' and (resid 1 through 26 )	B	B	1 - 26	1 - 26
15	15	chain 'B' and (resid 27 through 78 )	B	B	27 - 78	27 - 78
16	16	chain 'B' and (resid 79 through 101 )	B	B	79 - 101	79 - 101
17	17	chain 'B' and (resid 102 through 115 )	B	B	102 - 115	102 - 115
18	18	chain 'B' and (resid 116 through 127 )	B	B	116 - 127	116 - 127

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