PDB-5cse: Streptavidin-S112Y-K121E Complexed with Palladium-Containing Biot...

ID or keywords:

Entry

Database: PDB / ID: 5cse

Title

Streptavidin-S112Y-K121E Complexed with Palladium-Containing Biotin Ligand

Components

Streptavidin

Keywords

SUGAR BINDING PROTEIN / suzukiase / artificial metalloenzymes / beta barrel / dimer / biotin / palladium / Biotin-binding protein

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: 1.792 Å

Authors

Finke, A.D. / Vera, L. / Marsh, M. / Chatterjee, A. / Ward, T.R.

Citation

Journal: Chem Sci / Year: 2016
Title: An enantioselective artificial Suzukiase based on the biotin-streptavidin technology.
Authors: Chatterjee, A. / Mallin, H. / Klehr, J. / Vallapurackal, J. / Finke, A.D. / Vera, L. / Marsh, M. / Ward, T.R.

History

Deposition	Jul 23, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 4, 2015	Provider: repository / Type: Initial release
Revision 2.0	Jul 11, 2018	Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author Item: _atom_site.occupancy / _citation.journal_id_ISSN ..._atom_site.occupancy / _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 / _citation_author.name
Revision 2.1	Jan 10, 2024	Group: 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5cse.cif.gz	110.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5cse_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5cse_full_validation.pdf.gz	1 MB	Display
Data in XML	5cse_validation.xml.gz	12 KB	Display
Data in CIF	5cse_validation.cif.gz	15.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cs/5cse ftp://data.pdbj.org/pub/pdb/validation_reports/cs/5cse	HTTPS FTP

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Related structure data

Related structure data	1luqS S: Starting model for refinement
Similar structure data	6y25-1 2wpu-1 6y2m-1 4cpe-1 1lcv-1 6y34-1 5vl8-1 6t32-1 6auh-1 6t2z-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

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

2

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	81.368, 81.460, 90.811
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-322- HOH

#1: Protein	Streptavidin Mass: 16646.047 Da / Num. of mol.: 2 / Fragment: UNP residues 37-158 / Mutation: S112Y-K121E 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-SVP / chloro{di-tert-butyl[2-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)ethyl]-lambda~5~-phosphanyl}(1-phenylprop-1-ene-1,3-diyl-kappa~2~C~1~,C~3~)palladium Mass: 673.606 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₉H₄₆ClN₃O₂PPdS
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.92 Å³/Da / Density % sol: 57.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 15-25% PEG 1500, 100mM SPG buffer (mixed succinic acid, sodium dihydrogen phosphate and glycine in the ratio 2:7:7; 75% at pH 4 and 25% at pH 10)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.792→48.622 Å / Num. obs: 53292 / % possible obs: 97.6 % / Redundancy: 11.8 % / R_merge(I) obs: 0.09 / Net I/σ(I): 18.18
Reflection shell	Resolution: 1.792→1.856 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.7346 / Mean I/σ(I) obs: 3.2 / % possible all: 89.28

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
PHASER		phasing
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1LUQ

1luq

Resolution: 1.792→48.622 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2558	2642	4.96 %	Every 10th reflection
R_work	0.2231	-	-	-
obs	0.2247	53233	97.22 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.792→48.622 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1823	0	60	50	1933

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1974
X-RAY DIFFRACTION	f_angle_d	1.11	2723
X-RAY DIFFRACTION	f_dihedral_angle_d	14.555	635
X-RAY DIFFRACTION	f_chiral_restr	0.047	301
X-RAY DIFFRACTION	f_plane_restr	0.004	339

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 (%)
1.7921-1.8247	0.3542	120	0.3423	2291	X-RAY DIFFRACTION	84
1.8247-1.8598	0.2902	133	0.2826	2525	X-RAY DIFFRACTION	92
1.8598-1.8977	0.3303	139	0.2608	2586	X-RAY DIFFRACTION	95
1.8977-1.939	0.3306	134	0.2582	2549	X-RAY DIFFRACTION	93
1.939-1.9841	0.2505	138	0.2585	2636	X-RAY DIFFRACTION	95
1.9841-2.0337	0.2832	141	0.2375	2643	X-RAY DIFFRACTION	98
2.0337-2.0887	0.2588	138	0.2425	2613	X-RAY DIFFRACTION	97
2.0887-2.1502	0.259	137	0.2352	2694	X-RAY DIFFRACTION	97
2.1502-2.2196	0.2847	145	0.2272	2724	X-RAY DIFFRACTION	98
2.2196-2.2989	0.2685	140	0.2232	2704	X-RAY DIFFRACTION	99
2.2989-2.391	0.2791	147	0.2316	2770	X-RAY DIFFRACTION	100
2.391-2.4998	0.2483	145	0.2161	2716	X-RAY DIFFRACTION	100
2.4998-2.6316	0.2495	143	0.2274	2701	X-RAY DIFFRACTION	100
2.6316-2.7964	0.287	145	0.2186	2723	X-RAY DIFFRACTION	100
2.7964-3.0123	0.2059	139	0.2059	2765	X-RAY DIFFRACTION	100
3.0123-3.3154	0.2605	143	0.2144	2705	X-RAY DIFFRACTION	100
3.3154-3.795	0.2435	143	0.2103	2756	X-RAY DIFFRACTION	100
3.795-4.7806	0.2116	136	0.193	2759	X-RAY DIFFRACTION	100
4.7806-48.6395	0.2519	136	0.22	2731	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	2.0489	-0.1007	0.0662	1.6743	-0.1629	3.8312	-0.0198	0.1761	0.2528	-0.0989	0.0957	-0.1044	-0.1155	0.2511	-0.0669	0.0935	-0.0304	0.0071	0.1288	0.0122	0.144	17.129	14.9689	23.0549
2	2.3801	0.5817	0.052	2.7452	-1.6319	4.918	0.0591	0.1009	0.2431	-0.1079	0.0178	0.0226	-0.1347	0.1137	-0.0835	0.1028	0.0095	0.0355	0.0794	-0.0186	0.14	11.6947	12.1189	27.4909
3	4.7093	1.3696	-0.5277	3.6411	-2.3973	4.1534	-0.0256	0.098	0.002	0.2289	0.214	0.4124	-0.0199	-0.1317	-0.1766	0.1003	0.003	0.0133	0.0961	-0.038	0.0703	4.7088	7.3469	30.0685
4	4.4346	-1.0439	0.2729	3.6884	0.1868	4.1733	-0.0585	0.1977	-0.2955	0.0217	0.0473	0.4772	-0.2189	-0.4076	-0.0592	0.1598	0.0274	0.0063	0.1215	-0.0229	0.2399	14.384	-10.5667	20.415
5	6.5866	2.4778	4.7162	4.9216	3.9112	8.2198	-0.3026	-0.0214	-0.1767	-0.3119	0.1966	-0.531	-0.317	0.281	0.135	0.143	0.0694	-0.0125	0.1508	-0.0291	0.2922	22.1429	-4.3652	24.6929
6	3.6117	0.1294	2.3208	1.9864	0.5181	2.2933	0.289	0.682	-0.1786	-0.1313	0.0846	0.1662	0.2467	0.5671	-0.4095	0.255	0.0309	0.0364	0.2287	-0.0226	0.1564	16.5436	-3.4545	12.6964
7	1.8077	0.1445	0.4293	1.0083	-0.9624	3.4249	0.0185	0.0103	-0.0407	0.1389	0.0128	0.0089	0.1392	0.1439	0.0035	0.1305	0.037	-0.0072	0.0999	0.0002	0.1469	17.0514	-1.0543	27.1936
8	2.1802	-0.2939	-0.6178	3.1875	-2.4145	5.8483	0.0839	0.203	-0.132	-0.04	0.1603	0.1588	0.0281	-0.0335	-0.1575	0.0753	-0.0293	-0.003	0.0888	-0.0384	0.1314	14.582	1.1947	14.3748
9	4.8984	6.9477	-2.3508	9.8571	-3.3363	1.1293	-0.0188	-1.0711	-1.6053	1.058	-0.5241	-0.2027	1.8473	-1.2054	0.5914	0.5424	-0.0839	0.016	0.2958	0.0667	0.4011	11.3897	-16.5535	31.6887
10	3.2122	-1.0179	0.7359	5.0936	-2.0852	4.5017	-0.0948	0.5906	0.2424	-0.4615	0.3646	0.2943	0.0606	-0.2369	-0.2069	0.1007	-0.0429	0.0002	0.2581	0.0396	0.16	4.5322	6.9169	15.3415
11	5.452	-3.4305	1.4947	2.6976	-2.3109	3.9002	0.1167	0.3652	-0.7315	-0.1926	-0.0386	0.5877	0.2845	0.0823	-0.0775	0.1734	-0.0354	0.0304	0.1623	-0.0511	0.2133	7.7133	-7.2278	20.1217

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 16 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 112 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 113 through 133 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 16 through 27 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 28 through 37 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 38 through 52 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 53 through 78 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 79 through 97 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 98 through 102 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 103 through 122 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 123 through 134 )

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