PDB-6m9b: Wild-type streptavidin in complex with biotin solved by native SA...

ID or keywords:

Entry

Database: PDB / ID: 6m9b

Title

Wild-type streptavidin in complex with biotin solved by native SAD with data collected at 6 keV

Components

Streptavidin

Keywords

STRUCTURAL PROTEIN /

tetramer / biotin binder /

wild type /

ligand

Function / homology

Function and homology information

biotin binding / extracellular region
Similarity search - Function

Biological species

Streptomyces avidinii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.548 Å

Authors

Finke, A.D.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source.
Authors: Basu, S. / Finke, A. / Vera, L. / Wang, M. / Olieric, V.

History

Deposition	Aug 23, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 17, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2019	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6m9b.cif.gz	278.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6m9b.ent.gz	232.1 KB	Display	PDB format
PDBx/mmJSON format	6m9b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/6m9b ftp://data.pdbj.org/pub/pdb/validation_reports/m9/6m9b	HTTPS FTP

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Related structure data

Similar structure data	1df8-1 1lcw-1 4oka-1 6vp1-d 4cpi-1 2izh-1 4cpe-1 6vp2-d 6vjl-1 1rxh-1 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

C: Streptavidin

D: Streptavidin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.978, 98.322, 52.795
Angle α, β, γ (deg.)	90.00, 112.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Streptavidin / Mass: 13281.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical	ChemComp-BTN / BIOTIN / Biotin Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₂O₃S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.49 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 13.25mg SAV WT + 0.610mg biotin in 500uL H2O in the well: 500uL => 50% MPD sitting drops: 1uL SAV-biot + 1uL 80% MPD, 100mM MMT pH 5.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1, 2.075

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 11, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	2.075	1

Reflection

Resolution: 1.548→49.16 Å / Num. obs: 69231 / % possible obs: 99.33 % / Redundancy: 6.7 % / Net I/σ(I): 22.3

Reflection shell

Resolution: 1.548→1.604 Å

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 1.548→49.16 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 17.82

	R_factor	Num. reflection	% reflection
R_free	0.1834	3464	5 %
R_work	0.1536	-	-
obs	0.1551	136282	98.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.548→49.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3569	0	64	506	4139

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3785
X-RAY DIFFRACTION	f_angle_d	1.368	5200
X-RAY DIFFRACTION	f_dihedral_angle_d	13.424	1262
X-RAY DIFFRACTION	f_chiral_restr	0.058	589
X-RAY DIFFRACTION	f_plane_restr	0.005	650

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 (%)
1.5484-1.566	0.2695	170	0.254	3313	X-RAY DIFFRACTION	76
1.566-1.5845	0.235	229	0.234	4351	X-RAY DIFFRACTION	100
1.5845-1.6038	0.2899	232	0.2302	4385	X-RAY DIFFRACTION	100
1.6038-1.6241	0.2344	223	0.2209	4289	X-RAY DIFFRACTION	100
1.6241-1.6454	0.2651	232	0.2111	4409	X-RAY DIFFRACTION	99
1.6454-1.668	0.2253	229	0.2035	4316	X-RAY DIFFRACTION	100
1.668-1.6918	0.2232	233	0.1954	4420	X-RAY DIFFRACTION	100
1.6918-1.7171	0.2079	225	0.1923	4277	X-RAY DIFFRACTION	100
1.7171-1.7439	0.1988	228	0.1889	4344	X-RAY DIFFRACTION	100
1.7439-1.7725	0.2118	227	0.1828	4300	X-RAY DIFFRACTION	100
1.7725-1.8031	0.2134	233	0.1788	4417	X-RAY DIFFRACTION	100
1.8031-1.8359	0.1979	226	0.164	4342	X-RAY DIFFRACTION	100
1.8359-1.8712	0.1749	228	0.1613	4363	X-RAY DIFFRACTION	100
1.8712-1.9094	0.1711	229	0.1598	4344	X-RAY DIFFRACTION	100
1.9094-1.9509	0.1855	232	0.1583	4369	X-RAY DIFFRACTION	100
1.9509-1.9963	0.1841	227	0.1539	4327	X-RAY DIFFRACTION	100
1.9963-2.0462	0.209	232	0.1496	4398	X-RAY DIFFRACTION	100
2.0462-2.1015	0.1836	230	0.1507	4326	X-RAY DIFFRACTION	100
2.1015-2.1633	0.1928	227	0.1489	4319	X-RAY DIFFRACTION	100
2.1633-2.2332	0.1933	231	0.154	4398	X-RAY DIFFRACTION	100
2.2332-2.313	0.1999	229	0.1508	4339	X-RAY DIFFRACTION	100
2.313-2.4056	0.1934	230	0.1475	4384	X-RAY DIFFRACTION	100
2.4056-2.5151	0.181	229	0.1437	4350	X-RAY DIFFRACTION	100
2.5151-2.6477	0.195	228	0.1502	4335	X-RAY DIFFRACTION	100
2.6477-2.8135	0.2138	228	0.1503	4328	X-RAY DIFFRACTION	100
2.8135-3.0307	0.1842	225	0.1546	4349	X-RAY DIFFRACTION	99
3.0307-3.3357	0.1878	227	0.1503	4324	X-RAY DIFFRACTION	99
3.3357-3.8182	0.1574	231	0.1358	4353	X-RAY DIFFRACTION	99
3.8182-4.8099	0.1294	228	0.1167	4359	X-RAY DIFFRACTION	100
4.8099-49.1858	0.1558	236	0.1481	4340	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	2.0496	-0.4361	0.4152	2.1075	-0.2217	1.8402	-0.1265	-0.2787	0.0107	0.4157	0.1159	-0.1453	-0.0166	0.1261	0.0232	0.2906	0.0736	-0.0344	0.2077	-0.0011	0.1213	-0.9548	24.5883	77.2822
2	1.9058	-0.4639	0.0187	1.9988	-0.4111	2.0223	-0.1788	-0.1512	-0.026	0.2905	0.1224	-0.0874	0.0183	0.0671	0.0544	0.1648	0.0553	-0.0162	0.1217	0.0016	0.0805	-0.9529	21.536	70.4733
3	2.7121	1.7437	2.4397	2.9295	1.0999	4.2475	-0.1027	-0.0217	0.188	0.3042	0.142	-0.1586	-0.2743	0.2266	0.0402	0.1623	0.0237	-0.0247	0.1034	-0.0175	0.1478	-1.0682	30.2662	68.2016
4	6.9955	2.2763	2.1964	2.9963	0.1136	2.8015	-0.0564	-0.0758	0.0232	0.2019	0.1587	0.148	-0.073	-0.1858	-0.104	0.1232	0.0569	0.0238	0.1349	0.015	0.1022	-12.0243	26.8829	65.2318
5	1.0682	0.0598	-0.0418	2.0232	-0.6651	1.5385	-0.0425	0.0513	0.2446	0.2485	0.2052	0.1884	-0.3347	-0.2547	-0.1516	0.1885	0.045	0.0275	0.1279	0.0549	0.1834	-10.2574	47.9882	52.8313
6	2.5176	-0.0578	-0.8418	2.4662	-0.3253	2.3591	-0.0639	0.2136	0.2872	-0.0534	0.1686	0.017	-0.1544	-0.0373	-0.0797	0.1012	-0.0155	-0.0161	0.089	0.0364	0.1414	-4.7548	42.3488	46.7929
7	3.1496	-2.4129	-1.6682	5.5758	1.885	3.7492	0.0288	0.0125	0.1009	0.0368	0.0993	-0.002	-0.0783	-0.1111	-0.0898	0.0776	-0.0119	0.0027	0.0996	0.0206	0.0859	-5.1028	34.6886	52.736
8	1.7051	-1.1494	-0.1124	6.3262	1.2109	3.0152	-0.0224	-0.0285	0.3843	0.2773	0.1094	-0.251	-0.5253	0.0902	-0.105	0.2131	0.0018	-0.0134	0.1051	0.0099	0.1883	-3.5046	43.6796	58.9064
9	1.5353	-0.1298	0.3301	2.7245	-0.7855	3.2056	-0.0804	-0.0468	-0.2782	0.0013	0.1378	0.1903	0.5961	-0.0898	-0.078	0.2429	-0.0187	0.0406	0.1244	-0.0254	0.2285	-5.9636	7.0595	59.1441
10	1.578	-0.6057	-0.2036	1.6834	-0.1352	1.6498	-0.1384	-0.099	-0.246	0.0591	0.1215	0.1124	0.2567	-0.0413	0.0367	0.1749	0.0086	0.0199	0.0998	0.006	0.1684	-4.1175	11.819	62.6021
11	2.939	-0.1992	-0.0904	2.5116	-0.1504	1.7536	-0.1101	0.1138	-0.0388	-0.001	0.0733	-0.1906	0.2472	0.1442	0.0397	0.1511	0.0229	0.0082	0.0979	-0.0107	0.1155	2.9833	15.8552	58.9751
12	5.6174	2.2145	-0.0152	5.4889	-0.3087	2.7156	-0.1631	0.1961	-0.1445	-0.2248	0.1279	0.3942	0.3886	-0.344	0.0309	0.1511	-0.0456	-0.0084	0.1378	-0.0223	0.1316	-9.3483	16.108	56.3441
13	3.9167	2.4041	-0.1044	5.3201	-0.8498	0.9208	-0.1328	0.0255	0.1559	-0.1663	0.0406	-0.0695	-0.0557	-0.0223	0.1136	0.1222	0.0088	-0.001	0.1203	-0.0191	0.1086	0.9663	27.9481	55.6504
14	7.1321	-1.1637	-4.3585	4.1236	0.9472	3.3501	-0.4399	0.6889	-0.5981	-0.3467	0.0963	-0.3243	0.4984	0.3751	0.2514	0.3932	-0.0791	0.0791	0.2395	-0.0899	0.3452	-8.6828	3.9258	50.1845
15	0.355	-0.3645	0.6786	1.1611	-0.4244	1.3173	-0.0811	0.3412	0.0763	-0.328	0.2878	0.7021	0.0059	-0.4021	-0.1343	0.2056	-0.1081	-0.1696	0.3603	0.1821	0.2192	-21.033	33.4962	40.2331
16	2.5873	0.104	-0.0798	2.0392	-0.6083	1.2778	-0.018	0.267	0.0598	-0.2775	0.2517	0.2952	0.0586	-0.2977	-0.09	0.138	-0.0464	-0.0505	0.2456	0.0928	0.1589	-16.4019	35.5104	43.3571
17	2.0906	0.1063	-0.0209	1.5503	-1.0713	1.845	-0.1051	0.1187	0.025	0.0098	0.2857	0.3665	-0.0697	-0.4529	0.0077	0.1014	0.0097	-0.0116	0.1939	0.0936	0.1866	-18.3447	33.8352	53.3138
18	1.7833	-0.7553	1.111	1.8022	0.9304	6.5149	-0.0396	0.3038	-0.1487	-0.243	0.1695	0.5122	0.3347	-0.2495	-0.0298	0.1859	-0.1118	-0.0739	0.2306	0.0654	0.2037	-18.215	25.6137	46.7587

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 89 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 90 through 104 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 105 through 125 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 70 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 71 through 89 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 90 through 114 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 115 through 126 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 8 through 29 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 30 through 70 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 71 through 89 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 90 through 104 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 105 through 122 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 123 through 127 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 9 through 36 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 37 through 70 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 71 through 114 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 115 through 126 )

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