PDB-8qq3: Streptavidin with a Ni-cofactor

ID or keywords:

Entry

Database: PDB / ID: 8qq3

Title

Streptavidin with a Ni-cofactor

Components

Streptavidin

Keywords

METAL BINDING PROTEIN / Artificial Metalloenzymes

Function / homology

Function and homology information

biotin binding / extracellular region
Similarity search - Function

Biological species

Streptomyces avidinii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Zhang, K. / Jakob, R.P. / Ward, T.R.

Funding support

Switzerland, 1items

Citation

Journal: Chem.Commun.(Camb.) / Year: 2024
Title: An artificial nickel chlorinase based on the biotin-streptavidin technology.
Authors: Yu, K. / Zhang, K. / Jakob, R.P. / Maier, T. / Ward, T.R.

History

Deposition	Oct 3, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 7, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 21, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qq3.cif.gz	219.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8qq3.ent.gz	176.8 KB	Display	PDB format
PDBx/mmJSON format	8qq3.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/qq/8qq3 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/8qq3	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Streptavidin

B: Streptavidin

C: Streptavidin

D: Streptavidin

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	115.028, 88.712, 57.790
Angle α, β, γ (deg.)	90.00, 97.13, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-359- HOH
2	1	D-371- HOH

#1: Protein	Streptavidin Mass: 16569.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22629
#2: Chemical	ChemComp-WKF / 4-[4-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]butylamino]-~{N}1,~{N}1'-di(quinolin-8-yl)cyclohexane-1,1-dicarboxamide Mass: 637.794 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₃₅H₃₉N₇O₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.21 Å³/Da / Density % sol: 44.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 0.1 M Tris, pH 8.5, 30% w/v PEG 4K

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→46.13 Å / Num. obs: 75827 / % possible obs: 99.85 % / Redundancy: 6.9 % / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.027 / R_rim(I) all: 0.072 / Net I/σ(I): 14.5
Reflection shell	Resolution: 1.6→1.657 Å / R_merge(I) obs: 1.236 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7553 / CC_1/2: 0.735 / CC star: 0.92 / R_pim(I) all: 0.499 / R_rim(I) all: 1.335

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→46.13 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1906	3835	5.06 %
R_work	0.1616	-	-
obs	0.163	75725	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.6→46.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3758	0	156	394	4308

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4162
X-RAY DIFFRACTION	f_angle_d	1.215	5722
X-RAY DIFFRACTION	f_dihedral_angle_d	14.27	767
X-RAY DIFFRACTION	f_chiral_restr	0.065	614
X-RAY DIFFRACTION	f_plane_restr	0.007	762

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 (%)
1.6-1.62	0.3378	151	0.332	2659	X-RAY DIFFRACTION	100
1.62-1.64	0.322	153	0.3118	2615	X-RAY DIFFRACTION	100
1.64-1.66	0.3229	151	0.2944	2646	X-RAY DIFFRACTION	100
1.66-1.69	0.296	147	0.2675	2637	X-RAY DIFFRACTION	100
1.69-1.71	0.2994	136	0.2529	2661	X-RAY DIFFRACTION	100
1.71-1.74	0.2732	150	0.2502	2634	X-RAY DIFFRACTION	100
1.74-1.77	0.2908	138	0.2266	2666	X-RAY DIFFRACTION	100
1.77-1.8	0.2864	140	0.2267	2650	X-RAY DIFFRACTION	100
1.8-1.83	0.2821	144	0.214	2632	X-RAY DIFFRACTION	100
1.83-1.87	0.2142	153	0.196	2673	X-RAY DIFFRACTION	100
1.87-1.9	0.2028	146	0.1777	2630	X-RAY DIFFRACTION	100
1.9-1.95	0.1925	162	0.169	2627	X-RAY DIFFRACTION	100
1.95-1.99	0.1847	147	0.1579	2654	X-RAY DIFFRACTION	100
1.99-2.04	0.1867	117	0.1559	2672	X-RAY DIFFRACTION	100
2.04-2.1	0.2174	152	0.156	2662	X-RAY DIFFRACTION	100
2.1-2.16	0.1772	139	0.1565	2675	X-RAY DIFFRACTION	100
2.16-2.23	0.1712	144	0.1535	2638	X-RAY DIFFRACTION	100
2.23-2.31	0.1866	130	0.1564	2690	X-RAY DIFFRACTION	100
2.31-2.4	0.1963	138	0.1602	2671	X-RAY DIFFRACTION	100
2.4-2.51	0.2149	111	0.1581	2706	X-RAY DIFFRACTION	100
2.51-2.64	0.1618	143	0.1517	2651	X-RAY DIFFRACTION	100
2.64-2.81	0.1838	160	0.1459	2621	X-RAY DIFFRACTION	100
2.81-3.02	0.1628	137	0.1452	2734	X-RAY DIFFRACTION	100
3.02-3.33	0.1693	121	0.1483	2669	X-RAY DIFFRACTION	100
3.33-3.81	0.1918	132	0.1462	2695	X-RAY DIFFRACTION	100
3.81-4.8	0.1532	142	0.1249	2701	X-RAY DIFFRACTION	100
4.8-46.13	0.1797	151	0.174	2721	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	4.5025	1.2458	0.7737	7.5169	-1.7751	7.5103	0.1973	-0.3469	-0.9837	0.3197	0.0064	-0.3823	1.1954	0.3086	-0.1504	0.3755	0.0922	-0.0323	0.5286	0.0711	0.4721	48.7344	-35.0604	34.2955
2	2.929	0.2469	-0.0129	1.5743	0.7216	2.462	0.1011	0.0594	0.1252	-0.0476	-0.0491	-0.2334	-0.2216	0.1869	-0.0271	0.1979	0.0096	0.0165	0.2681	0.0132	0.2982	46.3047	-21.6541	31.9547
3	3.5525	3.4333	-1.2062	4.0406	-0.5603	0.9293	0.1014	0.6428	0.1725	0.1588	-0.5489	-0.1198	-0.3105	-0.2689	0.3137	0.5442	0.0139	0.0898	0.5189	0.0969	0.6034	43.0523	-8.0995	30.4872
4	2.0909	-1.1406	0.3847	2.7293	-0.389	1.4814	0.0407	0.0498	0.0593	-0.0341	-0.1137	-0.1987	0.0101	0.1128	0.0166	0.1972	-0.0148	0.0322	0.2126	-0.0103	0.2156	36.4226	-20.7868	31.5291
5	8.0254	-3.2469	-0.6929	3.3238	0.9817	3.1701	0.141	0.4944	0.3607	-0.0748	-0.1273	-0.3754	-0.0106	0.4107	-0.0388	0.2205	-0.0062	0.0417	0.2436	0.038	0.2296	40.2948	-20.425	23.106
6	1.4545	1.243	1.6202	1.6058	2.0119	2.5306	-0.3807	0.7546	1.3396	-0.4453	-0.0693	0.3743	-1.1621	0.163	0.5793	0.677	0.1136	-0.0038	0.5736	0.1203	0.5555	22.9274	-10.2685	-0.6425
7	2.8684	-0.5643	0.1721	2.208	-0.3969	3.3639	-0.0081	0.1382	-0.3498	-0.0088	0.0611	0.0285	0.2915	0.0775	0.0057	0.2792	0.0304	0.0082	0.2797	-0.0419	0.206	23.3136	-26.9633	4.0337
8	1.886	0.4886	-0.1038	3.0425	-0.8033	1.9669	0.1022	0.1034	-0.0754	-0.1548	-0.0887	-0.0401	0.066	0.0481	-0.0324	0.2254	0.0246	0.007	0.2168	-0.0278	0.1998	21.2982	-24.0989	12.9431
9	3.45	1.5839	-1.3722	2.518	-1.1692	0.7066	-0.259	0.1255	-0.243	-0.3171	0.1275	-0.1996	0.6948	0.3423	0.2196	0.2927	0.0241	0.028	0.2937	-0.0477	0.2395	30.5838	-25.1714	11.2704
10	7.0642	-4.5144	0.7382	7.218	-4.6348	8.5894	0.4219	-0.1752	-0.6871	-0.7326	0.5083	1.2439	1.1222	-0.3504	-0.8816	0.4452	-0.1014	-0.0796	0.4543	0.0377	0.5085	0.5029	-31.0244	15.5599
11	2.0885	0.0178	-0.2694	1.9012	0.0154	1.6258	0.0699	0.039	0.0413	-0.0814	-0.0629	0.2453	0.0121	-0.2861	-0.0012	0.1922	0.0064	0.0013	0.2495	-0.015	0.2234	9.3409	-17.9838	16.9834
12	1.4656	-1.3479	-0.4215	1.393	0.5311	3.8229	0.1315	-0.2924	-0.0406	0.2405	-0.1461	0.3532	0.2098	-0.4334	0.0446	0.1915	-0.0319	0.0261	0.2682	-0.011	0.2193	12.3421	-21.7353	24.7795
13	6.4719	2.6713	-0.8302	2.9337	-0.7745	2.539	0.0938	-0.3701	0.2983	-0.0541	-0.1135	-0.0234	-0.1451	0.059	-0.0119	0.2041	0.0125	0.0098	0.1419	-0.0295	0.1817	19.5473	-14.2094	23.0079
14	3.3234	-0.2541	0.3044	4.5935	0.5004	3.4483	-0.0333	-0.3907	0.3148	0.2374	0.1093	-0.1627	-0.3176	0.0047	-0.0838	0.3055	0.018	0.056	0.3301	-0.0288	0.2389	24.6043	-19.2293	47.7868
15	1.6248	-0.2808	-0.0668	2.8361	-0.1454	1.4617	0.0157	-0.2362	0.066	0.2148	0.0088	0.0849	-0.0515	-0.047	-0.03	0.2306	-0.0135	0.0185	0.2489	-0.0162	0.1869	28.8348	-24.4703	41.5313
16	2.8897	-1.7474	0.7847	4.3841	1.6935	2.6616	0.1339	-0.0008	-0.1587	-0.0641	-0.0505	0.0845	0.2412	-0.2421	0.0487	0.2103	-0.0396	-0.011	0.1453	0.0243	0.1874	25.1944	-29.4044	31.4166

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 10 through 17 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 18 through 44 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 45 through 53 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 54 through 122 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 123 through 134 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 10 through 17 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 18 through 53 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 54 through 122 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 123 through 134 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 10 through 17 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 18 through 97 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 98 through 112 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 113 through 135 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 10 through 27 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 28 through 112 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 113 through 135 )

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