PDB-9pua: L-Biotin-streptavidin binding

ID or keywords:

Entry

Database: PDB / ID: 9pua

Title

L-Biotin-streptavidin binding

Components

Streptavidin

Keywords

PROTEIN BINDING

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: 0.944 Å

Authors

Whitby, F.G.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Streptavidin Structures
Authors: Giesler, R. / Kay, M.S.

History

Deposition	Jul 30, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9pua.cif.gz	205 KB	Display	PDBx/mmCIF format
PDB format	pdb9pua.ent.gz		Display	PDB format
PDBx/mmJSON format	9pua.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9pua_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9pua_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9pua_validation.xml.gz	20.4 KB	Display
Data in CIF	9pua_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pu/9pua ftp://data.pdbj.org/pub/pdb/validation_reports/pu/9pua	HTTPS FTP

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Related structure data

Related structure data	9pubC C: citing same article (ref.)
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

J: Streptavidin

L: Streptavidin

hetero molecules

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

1

J: Streptavidin

L: Streptavidin

hetero molecules

J: Streptavidin

L: Streptavidin

hetero molecules

defined by author&software
54.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.688, 94.415, 105.140
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	J-22- TYR

#1: Protein	Streptavidin Mass: 13281.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical	ChemComp-A1CK6 / 5-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid / L-Biotin Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₂O₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.6 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 1 micro-liter protein containing 3 mM Biotin in 10 mM Tris-HCl pH 7.0 mixed with 1 micro-liter 38% Ammonium Sulfate, 100 mM Na-Acetate pH 4.5, 200 mM NaCl at 21C (294 K)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.96 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96 Å / Relative weight: 1
Reflection	Resolution: 0.94→41.886 Å / Num. obs: 139644 / % possible obs: 93.7 % / Redundancy: 35.1 % / CC_1/2: 1 / R_pim(I) all: 0.009 / Net I/σ(I): 31.4
Reflection shell	Resolution: 0.94→0.96 Å / Redundancy: 20.4 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5222 / CC_1/2: 0.449 / R_pim(I) all: 0.798 / % possible all: 71.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 0.944→41.886 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.976 / WR_factor R_free: 0.145 / WR_factor R_work: 0.123 / SU B: 0.412 / SU ML: 0.01 / Average fsc free: 0 / Average fsc work: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.018 / ESU R Free: 0.019
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1466	2769	1.992 %
R_work	0.1262	136221	-
all	0.127	-	-
obs	-	138990	93.465 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 12.615 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.439 Å²	0 Å²	0 Å²
2-	-	1.456 Å²	0 Å²
3-	-	-	-1.017 Å²

Refinement step

Cycle: LAST / Resolution: 0.944→41.886 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1815	0	38	299	2152

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.028	0.013	2207
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.019	2028
X-RAY DIFFRACTION	r_angle_refined_deg	2.473	1.682	3058
X-RAY DIFFRACTION	r_angle_other_deg	1.121	1.63	4567
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.198	5	296
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.118	22.447	94
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.297	15	291
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.708	15	9
X-RAY DIFFRACTION	r_chiral_restr	1.036	0.2	309
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	2672
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	559
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	332
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.218	0.2	1832
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	896
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	1122
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	148
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.875	0.2	42
X-RAY DIFFRACTION	r_nbd_other	0.439	0.2	108
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.291	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	3.389	0.985	1121
X-RAY DIFFRACTION	r_mcbond_other	3.059	0.982	1120
X-RAY DIFFRACTION	r_mcangle_it	3.843	1.464	1438
X-RAY DIFFRACTION	r_mcangle_other	3.862	1.468	1439
X-RAY DIFFRACTION	r_scbond_it	2.968	1.151	1079
X-RAY DIFFRACTION	r_scbond_other	2.966	1.151	1080
X-RAY DIFFRACTION	r_scangle_it	3.767	1.669	1613
X-RAY DIFFRACTION	r_scangle_other	3.766	1.669	1614
X-RAY DIFFRACTION	r_lrange_it	4.287	12.332	2335
X-RAY DIFFRACTION	r_lrange_other	4.286	12.329	2336
X-RAY DIFFRACTION	r_rigid_bond_restr	13.753	3	4227

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 (%)
0.944-0.968	0.508	163	0.517	7710	X-RAY DIFFRACTION	72.0048
0.968-0.995	0.342	175	0.338	8492	X-RAY DIFFRACTION	81.5641
0.995-1.023	0.281	166	0.254	8642	X-RAY DIFFRACTION	85.4068
1.023-1.055	0.2	196	0.174	8559	X-RAY DIFFRACTION	87.2881
1.055-1.089	0.151	163	0.123	8740	X-RAY DIFFRACTION	91.2847
1.089-1.128	0.116	184	0.098	8885	X-RAY DIFFRACTION	95.8668
1.128-1.17	0.117	172	0.091	8744	X-RAY DIFFRACTION	97.849
1.17-1.218	0.109	175	0.089	8446	X-RAY DIFFRACTION	98.4132
1.218-1.272	0.118	168	0.097	8157	X-RAY DIFFRACTION	98.7896
1.272-1.334	0.097	148	0.093	7848	X-RAY DIFFRACTION	98.9972
1.334-1.406	0.102	149	0.091	7468	X-RAY DIFFRACTION	99.1668
1.406-1.492	0.115	141	0.092	7074	X-RAY DIFFRACTION	99.531
1.492-1.595	0.112	121	0.093	6703	X-RAY DIFFRACTION	99.6495
1.595-1.722	0.101	135	0.096	6253	X-RAY DIFFRACTION	99.7813
1.722-1.887	0.114	122	0.099	5765	X-RAY DIFFRACTION	99.9491
1.887-2.109	0.133	101	0.106	5251	X-RAY DIFFRACTION	99.9067
2.109-2.435	0.15	109	0.119	4625	X-RAY DIFFRACTION	99.9789
2.435-2.981	0.162	88	0.14	3951	X-RAY DIFFRACTION	100
2.981-4.212	0.144	52	0.14	3115	X-RAY DIFFRACTION	100
4.212-41.886	0.253	41	0.208	1793	X-RAY DIFFRACTION	99.2962

Refinement TLS params.

S21: -0.0001 Å ° / T11: 0.0042 Å² / T12: 0 Å² / T23: 0 Å² / 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 °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T13 (Å²)	T22 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0001	-0.0003	-0.0001	0.0021	0.0004	0.0029	-0.0004	0	0.0001	0.0001	-0.0002	-0.0001	-0.0003	0.0003	-0.0001	0	0.0048	2.5792	33.4124	13.824
2	0.0051	0.001	0.0019	0.001	-0.0004	0.0015	0.0001	0.0001	0	0	0.0001	0.0004	0.0002	-0.0001	0	0.0002	0.0047	7.9867	17.992	11.1302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	J	14 - 135
2	X-RAY DIFFRACTION	2	ALL	L	15 - 135

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