PDB-7zlf: Mutant L39Y-L58F of recombinant bovine beta-lactoglobulin in comp...

ID or keywords:

Entry

Database: PDB / ID: 7zlf

Title

Mutant L39Y-L58F of recombinant bovine beta-lactoglobulin in complex with endogenous fatty acid

Components

Beta-lactoglobulin

Keywords

TRANSPORT PROTEIN / lactoglobulin / mutation / ligand

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 / Resolution: 2.1 Å

Authors

Loch, J.I. / Kurpiewska, K. / Bonarek, P.

Funding support

1items

Citation

Journal: J.Mol.Recognit. / Year: 2023
Title: beta-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies.
Authors: Bonarek, P. / Mularczyk, D. / Loch, J.I. / Kurpiewska, K. / Dziedzicka-Wasylewska, M.

History

Deposition	Apr 14, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 26, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Sep 20, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3	Feb 7, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4	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	7zlf.cif.gz	75.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7zlf.ent.gz		Display	PDB format
PDBx/mmJSON format	7zlf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7zlf_validation.pdf.gz	608.4 KB	Display	wwPDB validaton report
Full document	7zlf_full_validation.pdf.gz	608.2 KB	Display
Data in XML	7zlf_validation.xml.gz	8.9 KB	Display
Data in CIF	7zlf_validation.cif.gz	11.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zl/7zlf ftp://data.pdbj.org/pub/pdb/validation_reports/zl/7zlf	HTTPS FTP

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Related structure data

Related structure data	7z9zC 7za0C 7zcdC 1bsyS 7zdc C: citing same article (ref.) S: Starting model for refinement
Similar structure data	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

18.8 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
37.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.245, 53.245, 111.210
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-332- HOH

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Protein , 1 types, 1 molecules AAA

#1: Protein	Beta-lactoglobulin / Beta-LG Mass: 18317.047 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39Y, L58F 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 (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754

#1: Protein

Beta-lactoglobulin / Beta-LG

Mass: 18317.047 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39Y, L58F
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 (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754

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Non-polymers , 5 types, 66 molecules

#2: Chemical	ChemComp-DAO / LAURIC ACID Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.48 Å³/Da / Density % sol: 50.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.4 M 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: 1.54056 Å
Detector	Type: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 18, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54056 Å / Relative weight: 1
Reflection	Resolution: 2.1→15.21 Å / Num. obs: 11150 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.113 / R_rim(I) all: 0.122 / Net I/σ(I): 8.9
Reflection shell	Resolution: 2.1→2.16 Å / R_merge(I) obs: 1.046 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 898 / CC_1/2: 0.631 / R_rim(I) all: 1.181 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
CrysalisPro		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy

Resolution: 2.1→15.21 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.931 / SU B: 11.72 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.216 / ESU R Free: 0.186

	R_factor	Num. reflection	% reflection
R_free	0.2374	1052	9.454 %
R_work	0.1912	10076	-
all	0.196	-	-
obs	-	11128	99.357 %

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: 38.259 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.397 Å²	0.198 Å²	-0 Å²
2-	-	0.397 Å²	0 Å²
3-	-	-	-1.287 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→15.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1216	0	28	61	1305

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1261
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1245
X-RAY DIFFRACTION	r_angle_refined_deg	1.629	1.649	1696
X-RAY DIFFRACTION	r_angle_other_deg	1.248	1.583	2889
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.98	5	150
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.708	25.357	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.725	15	236
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.936	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	166
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1361
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	245
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	207
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	1097
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	564
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	648
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	49
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.234	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.193	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	2.013	3.101	609
X-RAY DIFFRACTION	r_mcbond_other	2.003	3.099	608
X-RAY DIFFRACTION	r_mcangle_it	3.17	4.627	756
X-RAY DIFFRACTION	r_mcangle_other	3.169	4.629	757
X-RAY DIFFRACTION	r_scbond_it	2.477	3.524	652
X-RAY DIFFRACTION	r_scbond_other	2.454	3.494	649
X-RAY DIFFRACTION	r_scangle_it	4.041	5.122	940
X-RAY DIFFRACTION	r_scangle_other	4.023	5.072	935
X-RAY DIFFRACTION	r_lrange_it	6.147	35.617	1275
X-RAY DIFFRACTION	r_lrange_other	6.125	35.544	1271

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
2.1-2.154	0.34	62	0.277	728	0.282	794	0.758	0.794	99.4962	0.268
2.154-2.211	0.296	77	0.268	702	0.271	784	0.81	0.827	99.3622	0.259
2.211-2.274	0.296	65	0.24	678	0.245	747	0.843	0.873	99.4645	0.228
2.274-2.343	0.289	57	0.247	665	0.25	725	0.879	0.883	99.5862	0.231
2.343-2.417	0.325	64	0.242	666	0.249	734	0.847	0.892	99.455	0.228
2.417-2.5	0.323	53	0.236	622	0.242	676	0.876	0.904	99.8521	0.213
2.5-2.592	0.288	68	0.197	595	0.206	663	0.909	0.933	100	0.188
2.592-2.694	0.297	59	0.212	586	0.22	646	0.919	0.932	99.8452	0.193
2.694-2.81	0.296	75	0.215	559	0.225	634	0.908	0.924	100	0.2
2.81-2.942	0.223	56	0.197	554	0.199	610	0.917	0.938	100	0.191
2.942-3.095	0.233	59	0.19	505	0.195	564	0.939	0.945	100	0.183
3.095-3.274	0.229	45	0.173	492	0.178	537	0.942	0.958	100	0.168
3.274-3.489	0.156	70	0.179	439	0.176	509	0.958	0.958	100	0.178
3.489-3.752	0.26	41	0.179	446	0.186	487	0.928	0.959	100	0.179
3.752-4.085	0.196	44	0.158	413	0.162	457	0.956	0.962	100	0.16
4.085-4.527	0.182	46	0.141	367	0.146	414	0.964	0.974	99.7585	0.144
4.527-5.152	0.18	32	0.146	346	0.149	378	0.966	0.977	100	0.153
5.152-6.136	0.296	32	0.193	294	0.202	326	0.934	0.96	100	0.201
6.136-8.047	0.241	28	0.198	244	0.203	272	0.924	0.955	100	0.206
8.047-15.21	0.263	19	0.197	174	0.204	198	0.96	0.966	97.4747	0.214

Refinement TLS params.

Method: refined / Origin x: -15.2183 Å / Origin y: 4.9196 Å / Origin z: 3.5662 Å

	11	12	13	21	22	23	31	32	33
T	0.0946 Å²	-0.0481 Å²	-0.0299 Å²	-	0.0347 Å²	0.0194 Å²	-	-	0.0199 Å²
L	0.1855 °²	0.0912 °²	0.4031 °²	-	1.085 °²	0.3023 °²	-	-	1.3017 °²
S	-0.0891 Å °	0.0734 Å °	0.0495 Å °	-0.0268 Å °	-0.0011 Å °	0.0997 Å °	-0.0366 Å °	0.1186 Å °	0.0903 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
3	X-RAY DIFFRACTION	1	ALL	AAA	202

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Protein , 1 types, 1 molecules AAA

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Non-polymers , 5 types, 66 molecules

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