PDB-7bf9: Mutant M107L of recombinant bovine beta-lactoglobulin in complex ...

ID or keywords:

Entry

Database: PDB / ID: 7bf9

Title

Mutant M107L 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: 1.8 Å

Authors

Loch, J.I. / Gotkowski, M. / 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 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	7bf9.cif.gz	75.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7bf9_validation.pdf.gz	628.9 KB	Display	wwPDB validaton report
Full document	7bf9_full_validation.pdf.gz	629.4 KB	Display
Data in XML	7bf9_validation.xml.gz	9.8 KB	Display
Data in CIF	7bf9_validation.cif.gz	13.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bf/7bf9 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/7bf9	HTTPS FTP

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Related structure data

Related structure data	7bf7C 7bf8C 7bgaC 7bgxC 7bgzC 7bh0C 1bsyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qi6-1 3ueu-1 4ib7-1 1b0o-1 4tlj-d 6fxb-2 5htd-1 4ib8-1 1yup-4 6fxb-1 4y0p-1 7bh0-1 1beb-d 3ph6-d 1yup-1 3ph5-d 4ib6-1 2blg-1 4ib9-1 6t44-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)	53.017, 53.017, 111.561
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: 18214.977 Da / Num. of mol.: 1 / Mutation: L1A, I2S, M107L 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.48 Å³/Da / Density % sol: 50.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1,34 M tri-sodium citrate in 0.5 Tris o 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: Dec 16, 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: 1.8→14.73 Å / Num. obs: 17194 / % possible obs: 99 % / Redundancy: 2.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.035 / R_pim(I) all: 0.025 / R_rim(I) all: 0.043 / Net I/σ(I): 13.8 / Num. measured all: 43886 / Scaling rejects: 200

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
1.8-1.84	2	0.428	2.2	1989	1019	0.351	0.414	0.597	2.2	99.9
9-14.73	2.6	0.015		291	111	0.999	0.009	0.018	36.7	69.4

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Processing

Software

Name	Version	Classification
Aimless	0.7.4	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: 1.8→14.157 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.939 / SU B: 5.226 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2232	1054	6.131 %	RANDOM
R_work	0.1837	16136	-	-
all	0.186	-	-	-
obs	0.18622	17190	98.341 %	-

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: 25.452 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.012 Å²	-0.006 Å²	-0 Å²
2-	-	-0.012 Å²	0 Å²
3-	-	-	0.039 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→14.157 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1196	0	19	158	1373

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1236
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1213
X-RAY DIFFRACTION	r_angle_refined_deg	1.602	1.657	1674
X-RAY DIFFRACTION	r_angle_other_deg	1.377	1.608	2801
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.26	5	152
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.307	25.385	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.618	15	224
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.646	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	166
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1364
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	244
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	221
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	1141
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	582
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	630
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	116
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.03	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.17	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	34
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.148	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	1.391	1.933	614
X-RAY DIFFRACTION	r_mcbond_other	1.387	1.932	613
X-RAY DIFFRACTION	r_mcangle_it	2.28	2.886	764
X-RAY DIFFRACTION	r_mcangle_other	2.28	2.887	765
X-RAY DIFFRACTION	r_scbond_it	1.834	2.208	621
X-RAY DIFFRACTION	r_scbond_other	1.832	2.209	622
X-RAY DIFFRACTION	r_scangle_it	3.019	3.208	910
X-RAY DIFFRACTION	r_scangle_other	3.017	3.209	911
X-RAY DIFFRACTION	r_lrange_it	5.783	24.459	1359
X-RAY DIFFRACTION	r_lrange_other	5.496	23.744	1329

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 (%)
1.8-1.846	0.31	66	0.265	1184	X-RAY DIFFRACTION	99.8403
1.846-1.896	0.285	83	0.252	1136	X-RAY DIFFRACTION	99.918
1.896-1.95	0.267	79	0.218	1104	X-RAY DIFFRACTION	100
1.95-2.009	0.288	49	0.199	1102	X-RAY DIFFRACTION	99.9132
2.009-2.073	0.254	66	0.189	1035	X-RAY DIFFRACTION	99.8187
2.073-2.145	0.238	66	0.184	1018	X-RAY DIFFRACTION	99.6324
2.145-2.224	0.234	72	0.192	984	X-RAY DIFFRACTION	99.7167
2.224-2.312	0.258	56	0.174	959	X-RAY DIFFRACTION	99.6075
2.312-2.413	0.215	49	0.169	920	X-RAY DIFFRACTION	99.2828
2.413-2.527	0.188	47	0.176	879	X-RAY DIFFRACTION	98.7207
2.527-2.659	0.256	57	0.188	824	X-RAY DIFFRACTION	98.5459
2.659-2.815	0.215	69	0.205	765	X-RAY DIFFRACTION	98.8152
2.815-3.001	0.255	55	0.213	732	X-RAY DIFFRACTION	98.2522
3.001-3.231	0.202	42	0.183	692	X-RAY DIFFRACTION	97.9973
3.231-3.522	0.207	46	0.178	659	X-RAY DIFFRACTION	97.1074
3.522-3.91	0.165	44	0.161	561	X-RAY DIFFRACTION	96.3376
3.91-4.463	0.228	44	0.139	513	X-RAY DIFFRACTION	95.3767
4.463-5.346	0.192	28	0.151	465	X-RAY DIFFRACTION	95.7281
5.346-7.108	0.201	18	0.2	360	X-RAY DIFFRACTION	93.1034
7.108-14.157	0.211	18	0.188	244	X-RAY DIFFRACTION	87.9195

Refinement TLS params.

Method: refined / Origin x: 15.0124 Å / Origin y: 4.5336 Å / Origin z: 33.5666 Å

	11	12	13	21	22	23	31	32	33
T	0.0356 Å²	0.0233 Å²	-0.0179 Å²	-	0.0307 Å²	-0.0255 Å²	-	-	0.0342 Å²
L	0.1024 °²	0.0693 °²	0.022 °²	-	0.8895 °²	-0.3805 °²	-	-	1.5919 °²
S	-0.0499 Å °	-0.0245 Å °	-0.0003 Å °	-0.0011 Å °	-0.0343 Å °	-0.0587 Å °	0.0078 Å °	-0.0825 Å °	0.0841 Å °

Refinement TLS group

Selection: ALL

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