PDB-6t31: Streptavidin variants harbouring an artificial organocatalyst bas...

ID or keywords:

Entry

Database: PDB / ID: 6t31

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: 1.35 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6t31.cif.gz	202.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6t31.ent.gz	136.1 KB	Display	PDB format
PDBx/mmJSON format	6t31.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/t3/6t31 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/6t31	HTTPS FTP

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Related structure data

Related structure data	6t1eSC 6t1gC 6t1kC 6t2lC 6t2yC 6t2zC 6t30C 6t32C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4cpe-1 2rtg-1 1lcv-1 6s50-d 2qcb-1 7kbz-d 5vcq-d 2rtb-1 6vjk-2 6vjk-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
68 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.377, 85.361, 100.383
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	A-308- HOH
2	1	A-363- HOH
3	1	B-399- HOH
4	1	B-404- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	ALA	ALA	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	16 - 38	16 - 38
1	2	GLY	GLY	VAL	VAL	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	41 - 55	41 - 55
1	3	GLY	GLY	ASP	ASP	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	58 - 67	58 - 67
1	4	GLY	GLY	ASN	ASN	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	70 - 82	70 - 82
1	5	ASN	ASN	THR	THR	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	85 - 91	85 - 91
1	6	GLY	GLY	GLU	GLU	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	94 - 101	94 - 101
1	7	ILE	ILE	ASN	ASN	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	104 - 105	104 - 105
1	8	TRP	TRP	TRP	TRP	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	108	108
1	9	THR	THR	ALA	ALA	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	111 - 114	111 - 114
1	10	ALA	ALA	HIS	HIS	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	117 - 127	117 - 127
1	11	PHE	PHE	THR	THR	(chain 'A' and (resid 16 through 39 or resid 41...	A	A	130 - 131	130 - 131
1	12	HL9	HL9	HL9	HL9	(chain 'A' and (resid 16 through 39 or resid 41...	A	C	201
2	13	GLY	GLY	ALA	ALA	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	16 - 38	16 - 38
2	14	GLY	GLY	VAL	VAL	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	41 - 55	41 - 55
2	15	GLY	GLY	ASP	ASP	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	58 - 67	58 - 67
2	16	GLY	GLY	ASN	ASN	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	70 - 82	70 - 82
2	17	ASN	ASN	THR	THR	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	85 - 91	85 - 91
2	18	GLY	GLY	GLU	GLU	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	94 - 101	94 - 101
2	19	ILE	ILE	ASN	ASN	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	104 - 105	104 - 105
2	20	TRP	TRP	TRP	TRP	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	108	108
2	21	THR	THR	ALA	ALA	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	111 - 114	111 - 114
2	22	ALA	ALA	HIS	HIS	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	117 - 127	117 - 127
2	23	PHE	PHE	THR	THR	(chain 'B' and (resid 16 through 39 or resid 41...	B	B	130 - 131	130 - 131
2	24	HL9	HL9	HL9	HL9	(chain 'B' and (resid 16 through 39 or resid 41...	B	D	201

#1: Protein	Streptavidin Mass: 16607.105 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-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
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 259 / 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: 1.86 Å³/Da / Density % sol: 33.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: CHES 0.1 M pH 9.5, 30% PEG 3000

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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: Jun 13, 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: 1.349→43.02 Å / Num. obs: 54426 / % possible obs: 99.92 % / Redundancy: 7.4 % / B_iso Wilson estimate: 18.61 Å² / CC_1/2: 0.999 / Net I/σ(I): 14.8
Reflection shell	Resolution: 1.349→1.397 Å / Num. unique obs: 5353 / CC_1/2: 0.609

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Processing

Software

Name	Version	Classification
Coot	1.16_3549	model building
PHENIX	1.16_3549	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6t1e

6t1e

Resolution: 1.35→43.02 Å / SU ML: 0.1498 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.9836

	R_factor	Num. reflection	% reflection
R_free	0.1654	2100	3.86 %
R_work	0.1382	-	-
obs	0.1392	54424	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 27.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→43.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1840	0	56	259	2155

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	2071
X-RAY DIFFRACTION	f_angle_d	1.0924	2856
X-RAY DIFFRACTION	f_chiral_restr	0.1902	309
X-RAY DIFFRACTION	f_plane_restr	0.0071	367
X-RAY DIFFRACTION	f_dihedral_angle_d	13.8585	1160

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	0.3221	137	0.2947	3412	X-RAY DIFFRACTION	99.41
1.38-1.42	0.3056	139	0.2641	3462	X-RAY DIFFRACTION	100
1.42-1.45	0.2563	138	0.2217	3441	X-RAY DIFFRACTION	100
1.45-1.5	0.2118	138	0.1782	3457	X-RAY DIFFRACTION	99.94
1.5-1.54	0.1972	140	0.1623	3481	X-RAY DIFFRACTION	99.97
1.54-1.6	0.1877	138	0.1509	3442	X-RAY DIFFRACTION	99.97
1.6-1.66	0.1688	139	0.1396	3462	X-RAY DIFFRACTION	100
1.66-1.74	0.1747	140	0.1363	3475	X-RAY DIFFRACTION	99.97
1.74-1.83	0.1664	139	0.1304	3474	X-RAY DIFFRACTION	100
1.83-1.95	0.158	139	0.1222	3462	X-RAY DIFFRACTION	99.83
1.95-2.1	0.1547	140	0.1222	3494	X-RAY DIFFRACTION	99.97
2.1-2.31	0.1552	141	0.1191	3520	X-RAY DIFFRACTION	100
2.31-2.64	0.1672	141	0.1256	3505	X-RAY DIFFRACTION	99.97
2.64-3.33	0.1545	143	0.1324	3556	X-RAY DIFFRACTION	100
3.33-43.02	0.152	148	0.1385	3681	X-RAY DIFFRACTION	99.87

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	5.66044244479	1.88759075334	1.99835792532	2.11442546333	1.01463020818	2.4717601153	-0.187730406494	-0.255800067888	0.145555667599	0.514485257452	0.18201175881	0.366411563576	-0.267544558986	-0.0782424387255	0.0608281406284	0.322092315169	0.0120466198758	0.0618866840209	0.277567043297	0.00927678491369	0.101589700675	-1.67266405307	-28.7257096432	-3.43918209507
2	1.47427769258	0.505263200433	0.283336983842	3.20639175016	-0.146267218872	1.74418788667	-0.0219323087567	-0.258792179875	0.108497599777	0.558867397799	-0.0263675473644	-0.133985669758	-0.160401948572	0.027812194807	0.0555659735573	0.236277179412	0.0051681706982	-0.0124515468775	0.231429308069	-0.000416923580575	0.116572196666	6.43581691956	-27.0031891782	-6.00616341019
3	1.71989174484	-0.770104244575	0.0934794824941	3.7681531181	-0.485264954258	1.79339363798	-0.00464871885684	-0.18430836743	-0.0817714298187	0.258398765918	-0.0523108112308	-0.12414044713	0.0382576541422	0.0328261919122	0.0435781918212	0.155271623065	-0.0076061931813	-0.00896370979168	0.187967299569	0.0226240792604	0.108827503429	6.67393260215	-33.640895338	-11.3523221378
4	3.41946289196	-0.444839914571	-0.66913613575	2.56228872669	-0.169524246685	2.54726658752	0.0717974873042	-0.122979227801	0.179978895637	0.319591573142	-0.0742991250003	0.176856514436	-0.180748553352	-0.303618625827	0.19911215384	0.143203314684	0.00305636354729	0.023924150456	0.159718985013	-0.00155761114078	0.0978865725498	-1.29353640553	-27.3071837096	-13.4310263024
5	4.20383433864	-2.34843299843	-1.34425894597	6.12752492399	2.6789270057	5.33890480209	0.117512287349	0.285580277383	-0.244700118572	-0.27992408561	-0.100377670435	-0.14057146052	0.271398041643	0.130281446658	-0.0131479558227	0.145137277495	0.00720450011569	-0.00380637398418	0.169345113674	0.00813406844063	0.151681973524	2.82151715934	-35.4254563339	-23.1519054085
6	7.79084243642	0.539493061066	0.655072112739	6.13415959876	-1.89703212498	5.6184779511	-0.470495846001	-0.995138356024	-1.45028225516	0.779965741435	-0.0793585782321	0.650972419119	0.393054051538	-0.589107298067	0.251711219518	0.382094570665	-0.00916464932376	0.217611535572	0.473102471192	0.0398052526217	0.312212692806	-7.65948769728	-30.4847575776	0.531445925775
7	2.18676746921	-0.263760551463	0.579661055481	5.01116243876	0.702242286811	3.35130309903	0.198932014953	0.145454510289	-0.0949725870957	-0.345566846875	-0.124211086195	0.913921182707	0.537333256548	-0.421905541883	0.0960813710789	0.15923787612	-0.0384896137796	-0.00411514833553	0.263631182907	-0.069190917471	0.380200209305	-24.9639600786	-31.7770863421	-28.4095720718
8	3.14201603263	-0.200248721565	0.125212821079	3.58396440032	0.565704429191	2.00068846969	-0.0803187574478	0.0320853990867	0.178381914279	-0.188662524941	-0.0801702814428	0.578468515122	-0.148055256218	-0.268616723722	0.148296475001	0.125819371626	0.0348274504102	-0.0228239143359	0.224976255887	-0.0261824508438	0.250480717861	-19.5890266963	-21.8324453986	-30.4515340674
9	1.46002789986	0.187550260224	0.343250007767	2.29605478551	0.628985316366	1.66020611475	-0.0104074052285	-0.0392875412054	0.0348450028452	-0.0375558067043	-0.0817711842974	0.35613698836	-0.000667959357902	-0.236121018819	-0.0427665728492	0.0940409841302	0.00977750980905	-0.00482402466178	0.173872264979	-0.0174866445318	0.156035170231	-13.9503346683	-27.3427672738	-30.4934708867
10	2.64893642345	0.872891783069	0.367725164951	4.63932051114	-0.886356989886	3.3590123035	-0.106229625038	0.275021814883	0.291207512834	-0.143406894134	-0.0622615935722	-0.252011057746	-0.271246676888	0.256588353561	0.0524426753984	0.135630775129	-0.00184971721817	-0.0234884608046	0.173423358465	0.00736005375671	0.153343384713	-1.70054216769	-19.312114597	-28.093249294
11	5.26255770751	-5.07623084625	-2.73479839626	5.3488655804	2.81506403991	7.53986946331	-0.0109881509079	-1.03210613639	0.767713541087	0.643088125486	0.424725391312	0.323141580914	-1.23320947461	-0.292416588071	-0.114592619657	0.425583053639	0.0153445895787	0.103407261622	0.442471702069	-0.0908803266243	0.391566859843	-24.1974799124	-24.8513529567	-17.6392173165

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 97 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 98 through 112 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 through 130 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 131 through 136 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 13 through 22 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 23 through 53 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 54 through 112 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 113 through 130 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 131 through 136 )

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Yorodumi