PDB-7bgz: Mutant L39K of recombinant beta-lactoglobulin in complex with end...

ID or keywords:

Entry

Database: PDB / ID: 7bgz

Title

Mutant L39K 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: 2.401 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	Nov 13, 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	7bgz.cif.gz	73.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7bgz_validation.pdf.gz	442 KB	Display	wwPDB validaton report
Full document	7bgz_full_validation.pdf.gz	442.5 KB	Display
Data in XML	7bgz_validation.xml.gz	8.6 KB	Display
Data in CIF	7bgz_validation.cif.gz	10.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bg/7bgz ftp://data.pdbj.org/pub/pdb/validation_reports/bg/7bgz	HTTPS FTP

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Related structure data

Related structure data	7bf7C 7bf8C 7bf9C 7bgaC 7bgxC 7bh0C 1bsyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bf8-d 5hte-1 2akq-1 4iba-1 4caj-1 7kp5-d 3fdx-d 6fu4-4 6jf5-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) #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)	53.560, 53.560, 110.880
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Beta-lactoglobulin / Beta-LG Mass: 18249.037 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39K 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): Origami B (DE3) / References: UniProt: P02754
#2: Chemical	ChemComp-DKA / DECANOIC ACID Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₀O₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.52 Å³/Da / Density % sol: 51.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 3.0 M ammonium sulfate in 0.5 M Tris-HCl pH 8.5

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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: Nov 6, 2014

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 2.4→14.26 Å / Num. obs: 7446 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.034 / R_rim(I) all: 0.067 / Net I/σ(I): 12.9 / Num. measured all: 26085 / Scaling rejects: 10

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.4-2.49	2.5	0.653	1.4	1866	754	0.714	0.502	0.83	1.4	97.6
8.98-14.26	2.2	0.015		271	123	1	0.012	0.02	35.7	71

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.4 Å	14.26 Å
Translation	2.4 Å	14.26 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: 2.401→13.753 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.918 / SU B: 21.452 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.297
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2663	1075	14.455 %	RANDOM
R_work	0.1938	6362	-	-
all	0.204	-	-	-
obs	0.20297	7437	97.279 %	-

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: 50.562 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.213 Å²	-0.106 Å²	-0 Å²
2-	-	-0.213 Å²	0 Å²
3-	-	-	0.69 Å²

Refinement step

Cycle: LAST / Resolution: 2.401→13.753 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1150	0	16	49	1215

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1183
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1157
X-RAY DIFFRACTION	r_angle_refined_deg	1.779	1.644	1598
X-RAY DIFFRACTION	r_angle_other_deg	1.233	1.58	2671
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.94	5	146
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.42	25	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.301	15	208
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.348	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	162
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1288
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	226
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	203
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	1014
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	514
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	576
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	43
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.137	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.243	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.108	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	2.46	3.533	596
X-RAY DIFFRACTION	r_mcbond_other	2.46	3.532	595
X-RAY DIFFRACTION	r_mcangle_it	3.972	5.264	738
X-RAY DIFFRACTION	r_mcangle_other	3.97	5.265	739
X-RAY DIFFRACTION	r_scbond_it	2.456	3.782	587
X-RAY DIFFRACTION	r_scbond_other	2.454	3.785	588
X-RAY DIFFRACTION	r_scangle_it	4	5.545	860
X-RAY DIFFRACTION	r_scangle_other	3.997	5.547	861
X-RAY DIFFRACTION	r_lrange_it	5.954	40.189	1175
X-RAY DIFFRACTION	r_lrange_other	5.95	40.127	1174

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
2.401-2.461	0.366	97	0.328	428	0.335	542	0.781	0.78	96.8635	0.315
2.461-2.527	0.348	58	0.287	437	0.294	513	0.694	0.804	96.4912	0.274
2.527-2.597	0.485	51	0.275	430	0.295	496	0.789	0.864	96.9758	0.252
2.597-2.674	0.361	66	0.279	438	0.29	519	0.825	0.864	97.1098	0.254
2.674-2.758	0.343	78	0.24	369	0.258	459	0.844	0.883	97.3856	0.213
2.758-2.851	0.337	67	0.225	394	0.241	473	0.86	0.895	97.463	0.201
2.851-2.954	0.279	76	0.204	368	0.216	453	0.901	0.926	98.0132	0.177
2.954-3.069	0.318	64	0.222	358	0.237	430	0.867	0.903	98.1395	0.2
3.069-3.198	0.285	54	0.21	356	0.221	418	0.9	0.916	98.0861	0.188
3.198-3.345	0.28	48	0.218	365	0.225	420	0.892	0.917	98.3333	0.201
3.345-3.514	0.291	48	0.205	319	0.216	373	0.903	0.931	98.3914	0.193
3.514-3.712	0.236	62	0.192	318	0.2	385	0.947	0.948	98.7013	0.181
3.712-3.948	0.26	43	0.19	295	0.199	342	0.925	0.946	98.8304	0.178
3.948-4.236	0.198	66	0.152	267	0.162	336	0.952	0.97	99.1071	0.142
4.236-4.596	0.151	42	0.114	259	0.12	302	0.979	0.98	99.6689	0.111
4.596-5.069	0.209	28	0.13	260	0.137	289	0.962	0.978	99.654	0.132
5.069-5.725	0.377	30	0.213	226	0.231	258	0.877	0.938	99.2248	0.205
5.725-6.726	0.419	33	0.214	201	0.238	237	0.861	0.938	98.7342	0.209
6.726-8.545	0.214	36	0.153	153	0.165	191	0.959	0.966	98.9529	0.159
8.545-13.753	0.227	26	0.184	117	0.193	150	0.953	0.965	95.3333	0.202

Refinement TLS params.

Method: refined / Origin x: 15.4893 Å / Origin y: 5.1748 Å / Origin z: 33.3413 Å

	11	12	13	21	22	23	31	32	33
T	0.3313 Å²	0.1697 Å²	-0.0061 Å²	-	0.1354 Å²	-0.0316 Å²	-	-	0.0201 Å²
L	0.8761 °²	0.4496 °²	0.77 °²	-	1.5374 °²	-0.4822 °²	-	-	2.6925 °²
S	-0.3844 Å °	-0.1764 Å °	-0.0333 Å °	0.1513 Å °	0.2618 Å °	-0.149 Å °	-0.2347 Å °	-0.407 Å °	0.1226 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	3 - 162
2	X-RAY DIFFRACTION	1	ALL	AaA	201

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