PDB-5myq: Crystal structure of avidin in complex with ferrocene homobiotin ...

ID or keywords:

Entry

Database: PDB / ID: 5myq

Title

Crystal structure of avidin in complex with ferrocene homobiotin derivative

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: 1.89 Å

Authors

Strzelczyk, P. / Bujacz, G.

Citation

Journal: To Be Published
Title: Structural investigation of the interactions of ferrocene homobiotin derivative with avidin.
Authors: Strzelczyk, P. / Plazuk, D. / Bujacz, G.

History

Deposition	Jan 27, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	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 1.2	Jan 17, 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 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5myq.cif.gz	211.8 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	1vyoS 3vgw 4i60 S: Starting model for refinement
Similar structure data	6xnd-d 3vgw-2 3vgw-1 1ldo-1 5irw-d 4jhq-1 3vhi-d 3vhh-d 2avi-1 5lur-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

62.6 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)	43.933, 82.081, 74.601
Angle α, β, γ (deg.)	90.00, 106.29, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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: Chemical

ChemComp-HBF / ferrocene homobiotin derivative

Mass: 401.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₁₇FeN₂OS

#3: 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 /

N-Acetylglucosamine

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

#4: Chemical

...
ChemComp-IOD / IODIDE ION /

Iodide

Mass: 126.904 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: I

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.25 Å³/Da / Density % sol: 45.32 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium iodide, 22 % w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.89→71.6 Å / Num. obs: 42387 / % possible obs: 97.1 % / Redundancy: 1.92 % / R_merge(I) obs: 0.052 / Net I/σ(I): 9.36
Reflection shell	Redundancy: 1.9 % / R_merge(I) obs: 0.423 / Mean I/σ(I) obs: 1.97 / % possible all: 94.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VYO

1vyo

Resolution: 1.89→71.6 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.938 / SU B: 7.551 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23201	1229	3.1 %	RANDOM
R_work	0.18567	-	-	-
obs	0.18711	38729	98.65 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 34.481 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.25 Å²	0 Å²	-0.65 Å²
2-	-	-2.08 Å²	-0 Å²
3-	-	-	1.04 Å²

Refinement step

Cycle: 1 / Resolution: 1.89→71.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3828	0	181	337	4346

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	4112
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3808
X-RAY DIFFRACTION	r_angle_refined_deg	2.185	1.939	5756
X-RAY DIFFRACTION	r_angle_other_deg	1.115	3	8740
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.412	5	484
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.508	23.721	172
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.088	15	676
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.482	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	636
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4532
X-RAY DIFFRACTION	r_gen_planes_other	0.002	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	1.264	1.832	1948
X-RAY DIFFRACTION	r_mcbond_other	1.261	1.83	1947
X-RAY DIFFRACTION	r_mcangle_it	2.133	2.729	2428
X-RAY DIFFRACTION	r_mcangle_other	2.134	2.731	2429
X-RAY DIFFRACTION	r_scbond_it	1.559	2.161	2164
X-RAY DIFFRACTION	r_scbond_other	1.558	2.162	2165
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.139	3.188	3173
X-RAY DIFFRACTION	r_long_range_B_refined	6.609	16.105	4613
X-RAY DIFFRACTION	r_long_range_B_other	6.609	16.112	4614
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.894→1.943 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	81	-
R_work	0.267	2650	-
obs	-	-	91.52 %

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	4.6588	-1.6991	1.3927	3.9226	-0.5061	4.1382	-0.063	0.1791	0.4196	0.1269	0.0221	-0.0873	-0.3227	-0.0741	0.0409	0.051	0.0118	0.0202	0.0256	0.0362	0.072	0.2209	58.9844	9.0705
2	5.0935	-0.2403	-0.4139	2.9603	0.0679	2.6316	0.0434	-0.0488	0.4886	0.1712	-0.0287	0.2987	-0.2993	-0.3476	-0.0148	0.0505	0.0473	0.0305	0.0632	0.0051	0.0989	-6.9273	55.5001	13.0805
3	2.1012	-0.9512	0.5622	6.587	-0.3061	2.732	-0.0421	0.0614	0.0131	0.1628	0.2043	-0.3739	0.1305	0.2607	-0.1622	0.0124	0.0189	-0.0173	0.0383	-0.0258	0.0364	5.0238	42.5177	13.7069
4	2.1752	-0.6628	0.6927	4.3417	-0.8551	2.1181	0.0249	0.2801	-0.1782	-0.2929	0.0276	0.3452	0.0011	-0.2428	-0.0525	0.0777	-0.005	-0.0486	0.1511	-0.038	0.0682	-11.4103	39.3536	1.8533
5	1.9242	-0.7313	0.0139	3.0263	0.0379	2.1994	0.0849	0.3346	-0.1232	-0.4612	0.0044	0.0233	0.0312	-0.0334	-0.0893	0.0726	-0.0113	-0.0024	0.0842	-0.0244	0.0122	-2.8666	39.9604	3.2343
6	1.9281	-0.5585	0.1628	4.9088	2.8396	6.9235	-0.0663	-0.2921	-0.0269	0.2951	0.2227	0.3569	0.0699	-0.1964	-0.1564	0.0201	0.0244	0.0288	0.0827	0.0455	0.0599	-9.1733	43.8084	19.0307
7	2.7361	-0.5108	0.308	4.5204	0.0046	6.3213	-0.0394	-0.1775	-0.2382	-0.1022	-0.0058	-0.1653	0.1916	0.1713	0.0452	0.1329	0.0266	-0.0157	0.0409	0.0603	0.1319	5.9857	22.9733	28.2173
8	5.5985	0.4004	-0.474	4.3869	-0.3021	3.4932	-0.016	-0.3251	-0.4134	0.1212	-0.0023	0.3515	0.4829	-0.3227	0.0182	0.0972	-0.0258	0.0307	0.0927	0.0608	0.0979	-1.794	26.6967	28.9122
9	3.3174	3.0405	0.0906	7.9244	-0.0276	2.1948	-0.0782	0.061	-0.0189	-0.1155	0.1488	-0.1596	-0.0229	0.1971	-0.0705	0.0281	0.0157	-0.0003	0.055	0.0135	0.04	7.6541	39.5353	21.6086
10	2.8552	-0.7326	-0.0742	4.0935	-0.5511	2.97	0.1075	-0.5906	-0.1847	0.408	-0.0101	0.2172	-0.0394	-0.1124	-0.0974	0.2132	0.0069	-0.0064	0.233	0.0009	0.0336	1.5382	42.6808	40.8854
11	3.7367	1.3966	-0.3779	3.4088	-0.026	2.0869	0.0122	-0.3872	-0.2073	0.4487	0.1077	-0.4193	-0.0048	0.1555	-0.12	0.0878	0.027	-0.047	0.1269	-0.0136	0.0614	7.563	42.0353	34.5955
12	4.0108	2.0397	2.4016	4.5963	2.6249	6.0411	-0.0894	-0.0967	-0.1726	0.116	0.1688	0.3779	-0.072	-0.5191	-0.0794	0.0157	0.0319	0.0362	0.1059	0.069	0.088	-6.9937	38.4945	25.7713

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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