PDB-6t2y: Streptavidin variants harbouring an artificial organocatalyst bas...

ID or keywords:

Entry

Database: PDB / ID: 6t2y

Title

Streptavidin variants harbouring an artificial organocatalyst based cofactor

Components

Streptavidin

Keywords

Biotin-binding protein / artificial cofactor /

streptavidin /

catalyst

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: 1.8 Å

Authors

Lechner, H. / Hocker, B.

Funding support

Austria, 1items

Citation

Journal: Chembiochem / Year: 2021
Title: An Artificial Cofactor Catalyzing the Baylis-Hillman Reaction with Designed Streptavidin as Protein Host*.
Authors: Lechner, H. / Emann, V.R. / Breuning, M. / Hocker, B.

History

Deposition	Oct 10, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 5, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 12, 2021	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
Revision 1.3	Jan 24, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6t2y.cif.gz	135.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6t2y.ent.gz	88.5 KB	Display	PDB format
PDBx/mmJSON format	6t2y.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/t2/6t2y ftp://data.pdbj.org/pub/pdb/validation_reports/t2/6t2y	HTTPS FTP

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Related structure data

Related structure data	6t1eSC 6t1gC 6t1kC 6t2lC 6t2zC 6t30C 6t31C 6t32C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6s50-d 6y3q-1 6aue-1 5vcq-d 4gjv-1 7kbz-d 5f2b-1 3rdu-2 6vp1-d 2qcb-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

hetero molecules

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

1

A: Streptavidin

B: Streptavidin

hetero molecules

A: Streptavidin

B: Streptavidin

hetero molecules

defined by author&software
Evidence: gel filtration
67.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.515, 84.449, 98.665
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-362- HOH

#1: Protein	Streptavidin / Mass: 16488.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-HL9 / 5-[(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]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide Mass: 403.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₉N₅O₂S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.82 Å³/Da / Density % sol: 32.29 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M di-Sodium hydrogen phosphate 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.8→47.54 Å / Num. obs: 41969 / % possible obs: 97.74 % / Redundancy: 7.6 % / CC_1/2: 0.985 / Net I/σ(I): 4.8
Reflection shell	Resolution: 1.8→1.864 Å / Num. unique obs: 4149 / CC_1/2: 0.229

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Processing

Software

Name	Version	Classification
PHENIX	1.17_3644	refinement
Coot		model building
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6t1e

6t1e

Resolution: 1.8→47.54 Å / SU ML: 0.2956 / Cross valid method: FREE R-VALUE / Phase error: 25.8768

	R_factor	Num. reflection	% reflection
R_free	0.2398	-	-
R_work	0.1933	-	-
obs	-	41969	97.74 %

Refinement step

Cycle: LAST / Resolution: 1.8→47.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1815	0	68	140	2023

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0041	1964
X-RAY DIFFRACTION	f_angle_d	0.7647	2682
X-RAY DIFFRACTION	f_chiral_restr	0.0499	289
X-RAY DIFFRACTION	f_plane_restr	0.0032	339
X-RAY DIFFRACTION	f_dihedral_angle_d	23.9516	295

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 (%)
1.8-1.84	0.3397	137	0.3657	2623	X-RAY DIFFRACTION	96.37
1.84-1.89	0.3475	145	0.339	2710	X-RAY DIFFRACTION	97.47
1.89-1.94	0.3466	132	0.3132	2611	X-RAY DIFFRACTION	97.37
1.94-2	0.355	138	0.3143	2702	X-RAY DIFFRACTION	97.8
2-2.06	0.2973	140	0.2814	2675	X-RAY DIFFRACTION	97.64
2.06-2.13	0.2983	137	0.2559	2640	X-RAY DIFFRACTION	97.06
2.13-2.22	0.2658	139	0.2346	2606	X-RAY DIFFRACTION	95.31
2.22-2.32	0.31	140	0.226	2685	X-RAY DIFFRACTION	98.36
2.32-2.44	0.2466	142	0.2118	2649	X-RAY DIFFRACTION	98.14
2.44-2.59	0.2332	137	0.2005	2688	X-RAY DIFFRACTION	97.99
2.6-2.8	0.2239	139	0.1989	2596	X-RAY DIFFRACTION	95.93
2.8-3.08	0.2505	144	0.1841	2686	X-RAY DIFFRACTION	98.33
3.08-3.52	0.2525	140	0.1669	2693	X-RAY DIFFRACTION	99.02
3.52-4.44	0.1919	137	0.1452	2680	X-RAY DIFFRACTION	97.34
4.44-47.54	0.1884	138	0.1518	2636	X-RAY DIFFRACTION	96.49

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	5.85944761137	2.02541815392	0.873632631051	8.11670248197	-0.236327021223	0.249732110079	-0.167031159295	0.902997704121	0.993635460928	-0.6695809309	-0.213804430679	0.665549997455	-0.429321299508	0.131142982047	-0.326766481266	0.619165005538	-0.0137092463234	-0.05421483277	0.456995693651	0.129618215691	0.313234757402	27.276447866	18.7766403071	-0.331458887836
2	0.397171279257	0.653417895218	-0.169607483025	1.20630240076	-0.0303720881537	0.546380775168	-0.360827705215	0.12371479862	0.365856591616	-0.619360123905	0.212819094968	0.178818961266	-0.618412647331	0.0812399272583	-0.151722490238	0.536029762616	0.0182929096519	-0.0606797680395	0.395140615103	0.0319947203363	0.28122398104	25.7162804753	14.066801754	3.90724982422
3	1.88991207735	0.204837445189	0.479119089814	1.15778707099	0.537037073743	2.79615555339	-0.0661452463079	0.23101166391	0.159416664386	-0.54287882381	-0.102182051246	0.252241415077	-0.12003073602	0.0557616895487	-0.0134758496712	0.359106833304	0.0085898188101	-0.0419322880608	0.318787557883	0.0517842420886	0.252098709053	22.9793244254	15.2559601324	7.34991242061
4	2.07614793221	-0.989066726001	0.488156964519	0.67120258976	0.533427241114	3.04765636715	0.0429398725487	0.128833714656	0.0406282347087	-0.0452813097412	-0.10521125038	0.333872158862	0.200687938227	-0.0947024957433	-0.000249309483318	0.335390127002	-0.0102541164066	0.00262335339622	0.31822652507	0.00854019875696	0.23015477021	21.9429623347	7.24469851108	11.2914561473
5	1.39704516087	-0.814323387015	0.584404996331	1.23447106439	0.180984456407	1.16276522853	0.0401318678346	0.0406370011172	0.402592288168	-0.27645706308	-0.228932775286	-0.210355300518	0.0209119781539	0.537865133702	0.00337913530591	0.341831961961	-0.0110776262129	0.0470523400776	0.36263035058	0.0711118295041	0.365022996388	31.359700949	16.7247093085	11.1002352556
6	1.02707442318	-0.336332797141	0.35627786584	0.182596275875	-0.194946800973	0.211858941576	0.236672934328	-0.852540959615	-0.311712109648	0.477756082789	-0.0396043732099	0.109100801252	1.10658749973	-0.593282922206	-0.0261932937132	0.491339674905	-0.165321573684	0.00401853968864	0.478737079029	-0.0155283591631	0.327766813883	20.4212984622	2.45115617411	30.4444666138
7	1.12705453097	-0.516403846797	0.614403237483	0.804966388802	0.135964022742	0.639167398754	-0.129434368361	0.340885017311	0.0718079664467	-0.328312630794	-0.0604426268657	-0.290832253255	0.0638909892503	0.382380449116	-0.0012727564993	0.396714869911	-0.00909656365193	0.075263632537	0.453595694688	0.0267673278636	0.355501557395	32.8297866566	11.70428251	10.0709331358
8	0.0248978509378	-0.0602086791769	0.0272296644765	1.00549896895	-1.30087753822	1.80384414923	-0.261986364896	-0.127804421088	-0.0533368608664	-0.0788772038521	0.176405769188	0.534534453536	-0.0391109476202	-0.85989872296	0.148211571301	0.179270869466	0.0322555529449	0.00375263980727	0.585426022077	-0.19090687692	0.496697117628	6.43476004039	16.960725237	23.9608680167
9	1.62256117009	0.471315334765	0.579155304857	2.18741437798	0.748953722303	2.0199498539	0.0371128159935	0.427963967408	-0.162680120235	-0.429511901591	0.0280348924964	0.412192808978	-0.0357700943777	-0.300728359497	-0.423627502548	0.254739690938	0.0947676049781	-0.176089951072	0.494885479606	-0.107509595723	0.475625283781	6.39487733598	14.110059481	15.3499577977
10	1.02738250304	-0.147675740744	0.799441632542	0.143444987932	0.344534816014	3.11761538749	-0.0798895293561	-0.126402204783	0.166855043128	-0.269812687907	-0.208606182795	0.526451385211	-0.130196825974	-0.623565442525	-0.0796900122599	0.245766386477	0.0382883412234	-0.0572499007168	0.404518941037	-0.040118962621	0.440978441188	12.0075258592	16.1624558269	17.4814371859
11	0.777987152811	-0.387269615254	0.0212116246724	0.287217656955	0.450086995791	2.27556280418	-0.321874490579	0.00474088307147	0.358063238257	-0.638149853773	0.280223422729	0.624920142407	-0.381141640048	-0.620100699091	-0.207493353344	0.362361440098	0.0639614851912	-0.14084458265	0.345566499347	0.0124022794739	0.476215287051	15.6821638396	23.4366061905	17.161825352
12	1.82387645534	-0.553671069683	1.03041856875	2.86733669418	0.333356281898	3.19966896781	-0.293547784113	-0.265229548364	-0.246939183941	0.00593212118054	-0.290899143916	-0.410619877234	-0.151591972619	-0.0949493216343	-0.118783738794	0.29067952773	0.0188991806642	-0.0232883406064	0.302975806011	0.0163733957358	0.329481524936	23.0095397295	20.2578307347	22.3798774913
13	0.487447092972	-0.196547250191	0.092267786841	1.17146513537	0.483374715338	1.15752819308	-0.415504408654	-0.207426995069	0.662152352766	0.0749941055048	0.0188151914516	0.595610117246	-0.00977683478751	-0.63750756614	-0.0255953048747	0.305672290939	0.0242143436306	-0.0229075908596	0.482604574261	-0.128930433978	0.458727075273	15.0157095235	19.0817842094	27.8167411025

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 78 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 79 through 97 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 98 through 112 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 113 through 122 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 123 through 135 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 14 through 27 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 37 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 38 through 78 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 79 through 97 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 98 through 122 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 123 through 134 )

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