PDB-5irw: Crystal structure of avidin in complex with 1-desthiobiotinylpyrene

ID or keywords:

Entry

Database: PDB / ID: 5irw

Title

Crystal structure of avidin in complex with 1-desthiobiotinylpyrene

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: 2.1 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	Oct 19, 2016	Group: Database references
Revision 1.2	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	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 1.4	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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5irw.cif.gz	210.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5irw.ent.gz	170.2 KB	Display	PDB format
PDBx/mmJSON format	5irw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5irw_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5irw_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5irw_validation.xml.gz	23.3 KB	Display
Data in CIF	5irw_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ir/5irw ftp://data.pdbj.org/pub/pdb/validation_reports/ir/5irw	HTTPS FTP

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Related structure data

Related structure data	5iruC 3vgwS 1vyo 4i60 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3vhm-d 2avi-1 3vgw-2 4jhq-1 5myq-d 3vhi-d 2c1s-1 1avd-1 3vgw-1 1y52-1 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: Avidin

B: Avidin

C: Avidin

D: Avidin

hetero molecules

59.9 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)	58.970, 81.520, 107.780
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: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 123 / Label seq-ID: 3 - 123

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	B	B
2	4	C	C
1	5	B	B
2	5	D	D
1	6	C	C
2	6	D	D

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-D9P / 1-desthiobiotinylpyrene

Mass: 398.497 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₆H₂₆N₂O₂

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.26 Å³/Da / Density % sol: 45.5 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Morpheus Screen (Molecular Dimensions) A1 solution (0.1 M IMIDAZOLE/MES MONOHYDRATE (ACID) BUFFER PH 6.5, 10% W/V POLYETHYLENE GLYCOL 20000, 20% V/V PEG 500 MME, 0.03 M MAGNESIUM CHLORIDE ...Details: Morpheus Screen (Molecular Dimensions) A1 solution (0.1 M IMIDAZOLE/MES MONOHYDRATE (ACID) BUFFER PH 6.5, 10% W/V POLYETHYLENE GLYCOL 20000, 20% V/V PEG 500 MME, 0.03 M MAGNESIUM CHLORIDE HEXAHYDRATE AND 0.03 M CALCIUM CHLORIDE DIHYDRATE), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.15K

Crystal

Density Matthews: 2.26 Å³/Da / Density % sol: 45.5 %

Crystal grow

Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus Screen (Molecular Dimensions) A1 solution (0.1 M IMIDAZOLE/MES MONOHYDRATE (ACID) BUFFER PH 6.5, 10% W/V POLYETHYLENE GLYCOL 20000, 20% V/V PEG 500 MME, 0.03 M MAGNESIUM CHLORIDE ...

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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: 2.1→50 Å / Num. obs: 30993 / % possible obs: 99.9 % / Redundancy: 6.53 % / R_merge(I) obs: 0.041 / Net I/σ(I): 24.34
Reflection shell	Redundancy: 6.79 % / R_merge(I) obs: 0.695 / Mean I/σ(I) obs: 3.35 / % possible all: 99.9

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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: 2.1→43.68 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.949 / SU B: 15.944 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23103	1551	5 %	RANDOM
R_work	0.19541	-	-	-
obs	0.19721	29440	99.86 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 67.376 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.64 Å²	-0 Å²	0 Å²
2-	-	0.45 Å²	-0 Å²
3-	-	-	0.2 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→43.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3784	0	151	112	4047

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	4031
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	3751
X-RAY DIFFRACTION	r_angle_refined_deg	1.956	1.929	5467
X-RAY DIFFRACTION	r_angle_other_deg	1.954	3	8616
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.443	5	482
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.733	24.048	168
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.26	15	665
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.744	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	630
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	4525
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	987
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	2.507	3.656	1937
X-RAY DIFFRACTION	r_mcbond_other	2.503	3.654	1936
X-RAY DIFFRACTION	r_mcangle_it	3.722	5.464	2416
X-RAY DIFFRACTION	r_mcangle_other	3.722	5.466	2417
X-RAY DIFFRACTION	r_scbond_it	3.183	4.112	2094
X-RAY DIFFRACTION	r_scbond_other	3.182	4.113	2095
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.682	6.045	3052
X-RAY DIFFRACTION	r_long_range_B_refined	7.808	31.842	4527
X-RAY DIFFRACTION	r_long_range_B_other	7.808	31.85	4528
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	12940	0.11
1	2	B	12940	0.11
2	1	A	13176	0.09
2	2	C	13176	0.09
3	1	A	12734	0.11
3	2	D	12734	0.11
4	1	B	13074	0.1
4	2	C	13074	0.1
5	1	B	13148	0.1
5	2	D	13148	0.1
6	1	C	12890	0.11
6	2	D	12890	0.11

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.463	113	-
R_work	0.441	2132	-
obs	-	-	99.96 %

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	5.1178	-0.0905	4.817	4.5165	-1.1681	8.7585	0.1056	0.4959	-0.3779	-0.3155	-0.0523	-0.4142	0.7238	0.4453	-0.0533	0.258	0.1448	0.0282	0.2986	-0.1781	0.199	33.455	-5.696	1.599
2	4.3667	0.0942	1.0477	8.3649	-0.9565	6.1918	-0.0422	1.0028	0.1512	-0.7996	0.2124	-0.5844	0.0481	0.4116	-0.1701	0.2006	0.0512	0.0146	0.324	-0.0449	0.1028	31.101	2.847	1.396
3	11.0825	1.3361	-1.898	3.9517	-0.6865	6.9686	0.6779	0.0296	-0.5558	0.3744	-0.2981	0.1782	0.7478	-0.299	-0.3799	0.2282	-0.0538	-0.0948	0.0444	-0.0045	0.0824	21.886	-3.112	15.033
4	5.6512	-0.9421	-2.7672	10.5484	3.4466	10.3178	-0.0376	0.682	0.1326	-0.7487	0.2526	0.6421	0.0732	-0.8628	-0.215	0.2065	0.0079	-0.2153	0.4227	-0.0391	0.2345	10.894	2.294	-1.379
5	5.4985	1.0805	-0.7269	8.3585	-0.6532	7.8887	-0.0779	0.4705	-0.536	-0.377	0.1961	0.4424	0.7081	-1.1768	-0.1181	0.2409	-0.0365	-0.1542	0.2375	-0.0746	0.188	13.544	-3.415	4.701
6	9.3689	3.659	2.2471	5.1566	1.8609	5.4895	0.1757	0.1262	0.352	-0.485	-0.168	0.1693	-0.3125	0.0223	-0.0077	0.1504	0.0499	-0.0163	0.0203	-0.0053	0.0249	23.08	10.623	8.572
7	3.3277	2.7513	2.1677	11.3659	3.3908	4.8981	-0.0804	-0.5448	0.178	1.0704	-0.0172	0.8789	0.2526	-1.0366	0.0976	0.287	-0.0503	0.2285	0.3508	-0.0567	0.2281	11.494	9.007	33.371
8	4.1435	-0.9457	1.4228	12.0098	-2.2192	5.851	-0.0066	-0.142	0.6155	0.5289	0.0541	0.8265	-0.5783	-1.0857	-0.0476	0.1963	0.0671	0.1102	0.2255	-0.0141	0.1996	13.905	14.832	27.163
9	9.6982	-3.2407	0.977	5.2306	-0.0879	5.5372	0.4545	0.4544	-0.3976	0.0248	-0.3086	0.2099	0.5725	-0.0956	-0.146	0.1724	-0.0162	-0.0351	0.034	-0.0171	0.0209	23.307	0.698	22.983
10	3.2162	1.2184	-1.0287	8.7858	-0.1569	6.8211	0.2359	-0.4304	-0.0571	0.9667	-0.3681	-0.6482	-0.386	0.1327	0.1322	0.2234	-0.049	-0.1504	0.0725	0.0055	0.128	34.156	17.045	29.321
11	1.6879	0.6175	-0.2064	9.9529	-3.3397	7.8759	-0.0341	-0.2762	-0.0002	0.8747	-0.0309	-0.7981	0.1743	0.216	0.065	0.2257	-0.0026	-0.1097	0.0594	-0.006	0.0762	31.626	8.677	29.749
12	15.635	-3.398	2.9547	5.7927	-0.8061	6.1205	0.4439	0.5697	0.1863	-0.2817	-0.2614	0.2911	-0.3211	-0.3864	-0.1825	0.1187	0.0522	-0.0004	0.0697	0.0171	0.0328	21.854	14.404	16.571

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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