PDB-5iru: Crystal structure of avidin in complex with 1-biotinylpyrene

ID or keywords:

Entry

Database: PDB / ID: 5iru

Title

Crystal structure of avidin in complex with 1-biotinylpyrene

Components

Avidin

Keywords

biotin binding protein / complex

Function / homology

Function and homology information

biotin binding / antibacterial humoral response / extracellular region
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Strzelczyk, P. / Bujacz, G.

Funding support

Poland, 2items

Citation

Journal: Molecules / Year: 2016
Title: Structural Characterization of the Avidin Interactions with Fluorescent Pyrene-Conjugates: 1-Biotinylpyrene and 1-Desthiobiotinylpyrene.
Authors: Strzelczyk, P. / Plazuk, D. / Zakrzewski, J. / Bujacz, G.

History

Deposition	Mar 14, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5iru.cif.gz	213.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5iru.ent.gz	172.6 KB	Display	PDB format
PDBx/mmJSON format	5iru.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ir/5iru ftp://data.pdbj.org/pub/pdb/validation_reports/ir/5iru	HTTPS FTP

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Related structure data

Related structure data	5irwC 3vgwS 1vyo 4i60 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1y55-1 2of8-1 3vhm-d 5irw-d 4zc6-d 2fhl-1 2of9-1 2avi-1 6bh9-d 1wbi-2 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: Avidin

B: Avidin

C: Avidin

D: Avidin

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	57.160, 81.950, 107.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	ARG	ARG	A	A	3 - 122	3 - 122
2	1	LYS	LYS	ARG	ARG	B	B	3 - 122	3 - 122
1	2	LYS	LYS	ARG	ARG	A	A	3 - 122	3 - 122
2	2	LYS	LYS	ARG	ARG	C	C	3 - 122	3 - 122
1	3	LYS	LYS	ARG	ARG	A	A	3 - 122	3 - 122
2	3	LYS	LYS	ARG	ARG	D	D	3 - 122	3 - 122
1	4	ARG	ARG	LEU	LEU	B	B	2 - 123	2 - 123
2	4	ARG	ARG	LEU	LEU	C	C	2 - 123	2 - 123
1	5	ARG	ARG	ARG	ARG	B	B	2 - 122	2 - 122
2	5	ARG	ARG	ARG	ARG	D	D	2 - 122	2 - 122
1	6	ARG	ARG	ARG	ARG	C	C	2 - 122	2 - 122
2	6	ARG	ARG	ARG	ARG	D	D	2 - 122	2 - 122

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein

Avidin

Mass: 14349.097 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural)

Gallus gallus (chicken) / References: UniProt: P02701

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Chemical

ChemComp-B9P / 1-biotinylpyrene

Mass: 428.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₆H₂₄N₂O₂S

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H₂O

Has protein modification

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: 2.2 Å³/Da / Density % sol: 44.12 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 28% w/v polyethylene glycol monomethyl ether 2000, 0.1 M Bis-Tris, 0.1 M trimethylamine hydrochloride

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.99999 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99999 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 34767 / % possible obs: 99.4 % / Redundancy: 6.41 % / R_merge(I) obs: 0.082 / Net I/σ(I): 12.48
Reflection shell	Redundancy: 6.62 % / R_merge(I) obs: 0.508 / Mean I/σ(I) obs: 3.61 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0107	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3VGW

3vgw

Resolution: 2→46.88 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.921 / SU B: 15.654 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.193 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26495	1739	5 %	RANDOM
R_work	0.22186	-	-	-
obs	0.22401	33028	99.39 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 53.584 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.33 Å²	0 Å²	-0 Å²
2-	-	-5.42 Å²	0 Å²
3-	-	-	-0.9 Å²

Refinement step

Cycle: 1 / Resolution: 2→46.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3828	0	180	227	4235

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	4108
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	3804
X-RAY DIFFRACTION	r_angle_refined_deg	1.979	1.937	5584
X-RAY DIFFRACTION	r_angle_other_deg	1.822	3	8732
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.241	5	484
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.629	23.721	172
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.763	15	676
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.802	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.164	0.2	636
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	4584
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	1020
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.817	2.044	1948
X-RAY DIFFRACTION	r_mcbond_other	1.808	2.042	1947
X-RAY DIFFRACTION	r_mcangle_it	3.127	3.041	2428
X-RAY DIFFRACTION	r_mcangle_other	3.128	3.044	2429
X-RAY DIFFRACTION	r_scbond_it	2.151	2.551	2160
X-RAY DIFFRACTION	r_scbond_other	2.151	2.551	2160
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.381	3.735	3157
X-RAY DIFFRACTION	r_long_range_B_refined	8.53	21.539	4867
X-RAY DIFFRACTION	r_long_range_B_other	8.529	21.547	4868
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	12788	0.09
1	2	B	12788	0.09
2	1	A	12968	0.08
2	2	C	12968	0.08
3	1	A	12768	0.1
3	2	D	12768	0.1
4	1	B	13154	0.09
4	2	C	13154	0.09
5	1	B	13074	0.08
5	2	D	13074	0.08
6	1	C	12918	0.1
6	2	D	12918	0.1

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.369	127	-
R_work	0.342	2402	-
obs	-	-	99.49 %

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	3.218	-1.9416	4.0571	6.0614	0.1314	12.5926	0.177	0.4084	-0.1432	-0.3247	-0.1698	-0.02	0.8777	0.5137	-0.0072	0.12	0.0344	0.0072	0.3154	-0.1283	0.1084	31.274	-5.131	0.896
2	5.5787	1.139	1.0248	10.8658	-0.3226	8.2342	-0.0776	0.3364	0.7663	-1.6789	0.2879	-0.5501	-0.1241	0.1553	-0.2102	0.28	0.0202	0.093	0.295	-0.0437	0.1892	28.598	2.923	1.089
3	11.7227	0.5141	-6.1376	2.0599	-1.2517	8.5393	-0.0426	-0.3497	-0.308	0.0451	0.0975	0.1612	0.3315	0.092	-0.055	0.0592	-0.0004	-0.0252	0.1769	-0.0141	0.0473	20.868	-3.687	15.203
4	3.3273	-1.7867	-2.8197	11.1318	6.4482	17.0019	-0.3611	0.7266	0.2484	-1.8397	0.0376	0.8194	-0.33	-1.4542	0.3235	0.474	-0.1178	-0.2371	0.5812	-0.0016	0.1338	8.354	1.712	-0.027
5	3.9597	0.6851	-0.494	8.9132	2.3399	8.3591	-0.123	0.3813	-0.3435	-0.1365	0.2194	0.4342	0.4507	-1.0152	-0.0964	0.0728	-0.0319	-0.0563	0.3849	-0.0618	0.1201	11.639	-4.365	5.411
6	8.6117	2.0812	2.1796	2.1751	1.1371	4.6375	0.2178	0.0977	0.7649	-0.14	-0.0232	0.1788	-0.6096	-0.3096	-0.1947	0.1217	0.0799	0.0763	0.2532	0.0104	0.1105	20.862	10.283	9.101
7	3.4099	1.0349	0.9294	8.5443	3.5215	9.3002	0.1869	0.075	0.2069	1.837	-0.2448	0.9493	0.0498	-0.4573	0.0578	0.4589	-0.0131	0.2346	0.3454	0.0008	0.1238	11.875	7.612	34.823
8	3.4494	-1.0646	1.6136	9.5636	-2.7385	6.0817	0.2852	0.0218	0.5427	1.1075	-0.0298	0.8629	-0.632	-0.6866	-0.2554	0.2255	0.0709	0.2039	0.3105	0.0333	0.2146	13.167	13.882	28.839
9	9.0518	-1.9526	-0.7473	2.9839	0.5051	2.9447	-0.0476	0.4234	-0.1351	0.1702	-0.0798	-0.0996	0.7016	-0.2876	0.1274	0.1722	-0.0724	0.0225	0.1663	0.0038	0.0189	22.769	-0.046	23.216
10	1.0612	1.7517	-0.8358	9.8392	1.4709	4.6267	0.1733	-0.1171	-0.1211	0.7906	-0.2286	-0.2257	-0.9572	0.5434	0.0554	0.4623	-0.1349	-0.0413	0.2159	-0.0537	0.0458	33.378	16.545	28.992
11	0.6704	-1.3346	0.5615	9.8021	-2.8724	6.8632	-0.0011	0.0149	0.0733	0.782	-0.0648	-0.6625	-0.0238	0.3241	0.066	0.0976	-0.0212	-0.064	0.1949	-0.0151	0.0574	31.428	7.963	29.872
12	12.1112	0.9289	3.4118	1.1138	0.85	4.205	-0.0393	0.009	0.2738	-0.3932	0.147	0.1868	-0.4156	-0.1729	-0.1077	0.1749	-0.0063	-0.0437	0.1647	0.0166	0.0791	20.194	13.805	17.304

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 46
2	X-RAY DIFFRACTION	2	A	47 - 95
3	X-RAY DIFFRACTION	3	A	96 - 121
4	X-RAY DIFFRACTION	4	B	3 - 46
5	X-RAY DIFFRACTION	5	B	47 - 95
6	X-RAY DIFFRACTION	6	B	96 - 121
7	X-RAY DIFFRACTION	7	C	3 - 46
8	X-RAY DIFFRACTION	8	C	47 - 95
9	X-RAY DIFFRACTION	9	C	96 - 121
10	X-RAY DIFFRACTION	10	D	3 - 46
11	X-RAY DIFFRACTION	11	D	47 - 95
12	X-RAY DIFFRACTION	12	D	96 - 121

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