PDB-7bh0: Mutant L39Y of recombinant beta-lactoglobulin in complex with end...

ID or keywords:

Entry

Database: PDB / ID: 7bh0

Title

Mutant L39Y of recombinant beta-lactoglobulin in complex with endogenous ligand

Components

Beta-lactoglobulin

Keywords

TRANSPORT PROTEIN / beta-lactoglobulin / lipocalin / mutation

Function / homology

Function and homology information

retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Loch, J.I. / Siuda, M.K. / Lewinski, K.

Funding support

Poland, 1items

Citation

Journal: Acta Biochim.Pol. / Year: 2021
Title: Interactions of new lactoglobulin variants with tetracaine: crystallographic studies of ligand binding to lactoglobulin mutants possessing single substitution in the binding pocket.
Authors: Loch, J. / Bonarek, P. / Siuda, M. / Wrobel, P. / Lewinski, K.

History

Deposition	Jan 9, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 31, 2021	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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 31, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7bh0.cif.gz	74.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7bh0_validation.pdf.gz	430.4 KB	Display	wwPDB validaton report
Full document	7bh0_full_validation.pdf.gz	430.8 KB	Display
Data in XML	7bh0_validation.xml.gz	9.1 KB	Display
Data in CIF	7bh0_validation.cif.gz	11.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bh/7bh0 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/7bh0	HTTPS FTP

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Related structure data

Related structure data	7bf7C 7bf8C 7bf9C 7bgaC 7bgxC 7bgzC 1bsyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bf9-1 3ueu-1 3ph5-d 4tlj-d 4ib6-1 6t44-d 1yup-4 4ib7-1 7bf8-d 1beb-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (5) #143 - Nov 2011 Toll-like Receptors similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

AAA: Beta-lactoglobulin

hetero molecules

18.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Beta-lactoglobulin

hetero molecules

AAA: Beta-lactoglobulin

hetero molecules

defined by author
Evidence: gel filtration
37 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.270, 53.270, 109.890
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	AAA-356- HOH
2	1	AAA-364- HOH

#1: Protein	Beta-lactoglobulin / Beta-LG Mass: 18283.031 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Origamiam B (DE3) / References: UniProt: P02754
#2: Chemical	ChemComp-DAO / LAURIC ACID Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₄O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.46 Å³/Da / Density % sol: 50.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 2.2 M ammonium sulfate in 0.5 M Tris-HCl pH 7.1

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å

Detector

Type: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 15, 2015

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 2.1→13.74 Å / Num. obs: 11001 / % possible obs: 99.4 % / Redundancy: 2.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.058 / R_pim(I) all: 0.038 / R_rim(I) all: 0.07 / Net I/σ(I): 7.7 / Num. measured all: 29177 / Scaling rejects: 29

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.1-2.16	2.1	0.223	2	896	0.884	0.199	0.3	98.5
8.66-13.74	2.2	0.033		140	0.996	0.025	0.041	72.6

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2 Å	13.66 Å
Translation	2 Å	13.66 Å

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Processing

Software

Name	Version	Classification
Aimless	0.3.11	data scaling
PHASER	2.5.6	phasing
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
CrysalisPro		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy

Resolution: 2.1→13.661 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.907 / SU B: 13.511 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.214
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2754	1066	9.708 %	RANDOM
R_work	0.2008	9915	-	-
all	0.208	-	-	-
obs	0.208	10981	99.133 %	-

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: 36.239 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.075 Å²	0.037 Å²	0 Å²
2-	-	0.075 Å²	-0 Å²
3-	-	-	-0.243 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→13.661 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1161	0	15	86	1262

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1195
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	1133
X-RAY DIFFRACTION	r_angle_refined_deg	1.686	1.641	1623
X-RAY DIFFRACTION	r_angle_other_deg	1.239	1.57	2613
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.219	5	149
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.049	25.098	51
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.547	15	198
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.997	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	165
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1327
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	235
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	208
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	1017
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	548
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	575
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	52
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.174	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.294	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.198	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	7.607	2.297	605
X-RAY DIFFRACTION	r_mcbond_other	7.603	2.296	604
X-RAY DIFFRACTION	r_mcangle_it	8.631	3.394	751
X-RAY DIFFRACTION	r_mcangle_other	8.625	3.395	752
X-RAY DIFFRACTION	r_scbond_it	10.248	2.857	590
X-RAY DIFFRACTION	r_scbond_other	10.24	2.857	591
X-RAY DIFFRACTION	r_scangle_it	11.433	4.014	872
X-RAY DIFFRACTION	r_scangle_other	11.427	4.015	873
X-RAY DIFFRACTION	r_lrange_it	11.807	28.085	1223
X-RAY DIFFRACTION	r_lrange_other	11.821	27.83	1214

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.1-2.153	0.285	71	0.241	692	0.245	782	0.878	0.877	97.5703	0.239
2.153-2.211	0.337	82	0.247	690	0.256	779	0.836	0.857	99.1014	0.239
2.211-2.273	0.309	55	0.242	649	0.248	706	0.847	0.876	99.7167	0.239
2.273-2.341	0.341	80	0.243	648	0.253	733	0.849	0.886	99.3179	0.234
2.341-2.415	0.333	67	0.237	647	0.246	714	0.869	0.898	100	0.23
2.415-2.497	0.357	70	0.239	611	0.252	682	0.837	0.87	99.8534	0.232
2.497-2.588	0.319	54	0.238	595	0.245	649	0.839	0.87	100	0.227
2.588-2.69	0.368	70	0.241	571	0.255	642	0.81	0.869	99.8442	0.233
2.69-2.805	0.325	49	0.248	575	0.254	624	0.796	0.864	100	0.24
2.805-2.935	0.309	66	0.216	516	0.226	582	0.884	0.915	100	0.216
2.935-3.086	0.318	56	0.22	502	0.23	558	0.866	0.907	100	0.218
3.086-3.263	0.289	49	0.223	496	0.229	545	0.891	0.917	100	0.223
3.263-3.474	0.262	51	0.201	456	0.207	507	0.92	0.938	100	0.204
3.474-3.733	0.244	46	0.189	431	0.194	477	0.92	0.948	100	0.196
3.733-4.059	0.195	48	0.167	405	0.17	453	0.963	0.959	100	0.175
4.059-4.488	0.218	37	0.139	373	0.146	410	0.951	0.967	100	0.147
4.488-5.092	0.227	29	0.139	340	0.145	369	0.957	0.973	100	0.152
5.092-6.03	0.304	27	0.2	298	0.207	325	0.922	0.961	100	0.201
6.03-7.802	0.255	25	0.189	255	0.195	280	0.947	0.961	100	0.196
7.802-13.661	0.208	34	0.153	161	0.162	203	0.959	0.973	96.0591	0.17

Refinement TLS params.

Method: refined / Origin x: 15.2489 Å / Origin y: 4.9936 Å / Origin z: 32.9951 Å

	11	12	13	21	22	23	31	32	33
T	0.2352 Å²	0.1014 Å²	-0.0414 Å²	-	0.0884 Å²	-0.0315 Å²	-	-	0.0423 Å²
L	0.3936 °²	-0.089 °²	0.757 °²	-	1.1622 °²	-0.451 °²	-	-	1.6331 °²
S	-0.1575 Å °	-0.1724 Å °	0.0288 Å °	0.0398 Å °	0.093 Å °	-0.2075 Å °	-0.1299 Å °	-0.3189 Å °	0.0646 Å °

Refinement TLS group

Selection: ALL

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