PDB-7bf7: Mutant L58F of recombinant bovine beta-lactoglobulin in complex w...

ID or keywords:

Entry

Database: PDB / ID: 7bf7

Title

Mutant L58F of recombinant bovine beta-lactoglobulin in complex with tetracaine

Components

Beta-lactoglobulin

Keywords

TRANSPORT PROTEIN / lactoglobulin / mutant / 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. / Kaczor, 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 1, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 13, 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 20, 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	7bf7.cif.gz	75.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7bf7_validation.pdf.gz	623.6 KB	Display	wwPDB validaton report
Full document	7bf7_full_validation.pdf.gz	623.8 KB	Display
Data in XML	7bf7_validation.xml.gz	8.9 KB	Display
Data in CIF	7bf7_validation.cif.gz	11.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bf/7bf7 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/7bf7	HTTPS FTP

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Related structure data

Related structure data	7bf8C 7bf9C 7bgaC 7bgxC 7bgzC 7bh0C 1bsyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4iba-1 3uew-1 2c98-d 4qnr-d 2vii-d 7bf8-d 7bgz-1 2akq-1 6rwr-1 4qnm-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

18.6 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
37.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.344, 53.344, 111.869
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: 18267.031 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L58F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Plasmid: pET-Duet / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Origami B(DE3) / References: UniProt: P02754
#2: Chemical	ChemComp-TE4 / Tetracaine / 2-(dimethylamino)ethyl 4-(butylamino)benzoate Mass: 264.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H₂O
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: 2.52 Å³/Da / Density % sol: 51.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.8 M ammonium sulfate in 0.5 M Tris-HCl pH 8.0

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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 4, 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: 2.1→13.77 Å / Num. obs: 11130 / % possible obs: 98.8 % / Redundancy: 2.6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.061 / R_pim(I) all: 0.041 / R_rim(I) all: 0.074 / Net I/σ(I): 7.9 / Num. measured all: 29028 / Scaling rejects: 15

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
2.1-2.17	2	0.285	1.6	1943	982	0.805	0.265	0.391	1.7	96.8
8.4-13.77	2.1	0.024		354	166	0.999	0.018	0.03	17.1	77.7

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy

Resolution: 2.1→13.769 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.92 / SU B: 12.777 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.196
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2491	1049	9.444 %	RANDOM
R_work	0.2029	10058	-	-
all	0.207	-	-	-
obs	0.20738	11107	98.37 %	-

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: 31.557 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.014 Å²	0.007 Å²	-0 Å²
2-	-	0.014 Å²	0 Å²
3-	-	-	-0.045 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→13.769 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1210	0	24	74	1308

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1255
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1223
X-RAY DIFFRACTION	r_angle_refined_deg	1.722	1.659	1699
X-RAY DIFFRACTION	r_angle_other_deg	1.232	1.606	2828
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.576	5	152
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.33	25.455	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.441	15	229
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.38	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	167
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1379
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	249
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	201
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	1082
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	560
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	601
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	63
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.201	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.212	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.743	2.556	614
X-RAY DIFFRACTION	r_mcbond_other	1.74	2.555	613
X-RAY DIFFRACTION	r_mcangle_it	2.88	3.821	764
X-RAY DIFFRACTION	r_mcangle_other	2.879	3.822	765
X-RAY DIFFRACTION	r_scbond_it	1.935	2.823	641
X-RAY DIFFRACTION	r_scbond_other	1.931	2.8	638
X-RAY DIFFRACTION	r_scangle_it	3.306	4.132	935
X-RAY DIFFRACTION	r_scangle_other	3.302	4.096	930
X-RAY DIFFRACTION	r_lrange_it	5.187	29.098	1278
X-RAY DIFFRACTION	r_lrange_other	5.157	28.969	1271

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.155	0.385	81	0.261	679	X-RAY DIFFRACTION	95.5975
2.155-2.213	0.336	86	0.267	716	X-RAY DIFFRACTION	99.0123
2.213-2.277	0.305	48	0.234	698	X-RAY DIFFRACTION	98.5469
2.277-2.347	0.332	57	0.244	700	X-RAY DIFFRACTION	99.0838
2.347-2.424	0.241	55	0.219	681	X-RAY DIFFRACTION	98.7919
2.424-2.509	0.309	77	0.244	599	X-RAY DIFFRACTION	98.2558
2.509-2.603	0.313	64	0.235	608	X-RAY DIFFRACTION	98.5337
2.603-2.709	0.278	64	0.234	586	X-RAY DIFFRACTION	98.1873
2.709-2.829	0.317	64	0.235	570	X-RAY DIFFRACTION	98.4472
2.829-2.967	0.265	49	0.223	562	X-RAY DIFFRACTION	98.8673
2.967-3.127	0.245	43	0.232	521	X-RAY DIFFRACTION	99.2958
3.127-3.315	0.255	50	0.216	515	X-RAY DIFFRACTION	99.8233
3.315-3.543	0.254	63	0.206	460	X-RAY DIFFRACTION	100
3.543-3.825	0.215	69	0.166	418	X-RAY DIFFRACTION	100
3.825-4.187	0.162	43	0.161	406	X-RAY DIFFRACTION	100
4.187-4.677	0.174	36	0.138	374	X-RAY DIFFRACTION	100
4.677-5.391	0.195	34	0.146	347	X-RAY DIFFRACTION	100
5.391-6.58	0.187	23	0.187	296	X-RAY DIFFRACTION	100
6.58-9.213	0.304	32	0.179	225	X-RAY DIFFRACTION	100
9.213-13.769	0.188	11	0.188	97	X-RAY DIFFRACTION	65.0602

Refinement TLS params.

Method: refined / Origin x: 15.082 Å / Origin y: 4.7599 Å / Origin z: 33.8706 Å

	11	12	13	21	22	23	31	32	33
T	0.0679 Å²	0.0415 Å²	-0.0181 Å²	-	0.0396 Å²	-0.0247 Å²	-	-	0.0184 Å²
L	0.3315 °²	0.048 °²	0.1986 °²	-	1.2209 °²	-0.3248 °²	-	-	1.1486 °²
S	-0.1228 Å °	-0.0649 Å °	0.0175 Å °	0.0118 Å °	0.0493 Å °	-0.0579 Å °	-0.0055 Å °	-0.0915 Å °	0.0735 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
4	X-RAY DIFFRACTION	1	ALL	AAA	301 - 374

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