PDB-7q19: Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with d...

ID or keywords:

Entry

Database: PDB / ID: 7q19

Title

Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#3)

Components

Beta-lactoglobulin

Keywords

TRANSPORT PROTEIN / lactoglobulin / mutation / desipramine

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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Loch, J.I. / Barciszewski, J. / Pokrywka, K. / Lewinski, K.

Funding support

1items

Citation

Journal: Iucrj / Year: 2022
Title: New ligand-binding sites identified in the crystal structures of [beta]-lactoglobulin complexes with desipramine
Authors: Loch, J.I. / Barciszewski, J. / Sliwiak, J. / Bonarek, P. / Wrobel, P. / Pokrywka, K. / Shabalin, I.G. / Minor, W. / Jaskolski, M. / Lewinski, K.

History

Deposition	Oct 18, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 11, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2	Nov 6, 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	7q19.cif.gz	78.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7q19.ent.gz		Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q1/7q19 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/7q19	HTTPS FTP

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Related structure data

Related structure data	7q17C 7q18C 7q2nC 7q2oC 7q2pC 1bsyS S: Starting model for refinement C: citing same article (ref.)
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) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

AAA: Beta-lactoglobulin

hetero molecules

18.9 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&software
Evidence: gel filtration
37.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.298, 66.298, 60.630
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	AAA-203- SO4
2	1	AAA-204- SO4
3	1	AAA-204- SO4
4	1	AAA-390- HOH
5	1	AAA-406- HOH
6	1	AAA-420- HOH

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Protein , 1 types, 1 molecules AAA

#1: Protein	Beta-lactoglobulin / Beta-LG Mass: 18279.965 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39A, I56F, M107W 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(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P02754

#1: Protein

Beta-lactoglobulin / Beta-LG

Mass: 18279.965 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39A, I56F, M107W
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(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P02754

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Non-polymers , 5 types, 127 molecules

#2: Chemical	ChemComp-DSM / 3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE / Desipramine;Norpramin Mass: 266.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₂₂N₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant, inhibitor*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.1 Å³/Da / Density % sol: 41.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.40 M (NH4)2SO4, 0.5 M Tris-HCl pH 8.5, desipramine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.55→41.69 Å / Num. obs: 22796 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC_1/2: 1 / R_rim(I) all: 0.051 / Net I/σ(I): 23.24
Reflection shell	Resolution: 1.55→1.64 Å / Redundancy: 9.11 % / Mean I/σ(I) obs: 1.98 / Num. unique obs: 3482 / CC_1/2: 0.087 / R_rim(I) all: 1.022 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy

Resolution: 1.55→41.69 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.954 / SU B: 4.015 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.094

	R_factor	Num. reflection	% reflection
R_free	0.2337	1000	4.387 %
R_work	0.1971	21796	-
all	0.199	-	-
obs	-	22796	99.917 %

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: 29.44 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.512 Å²	0.256 Å²	-0 Å²
2-	-	0.512 Å²	-0 Å²
3-	-	-	-1.66 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→41.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1254	0	37	120	1411

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1327
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1277
X-RAY DIFFRACTION	r_angle_refined_deg	1.629	1.645	1799
X-RAY DIFFRACTION	r_angle_other_deg	1.385	1.607	2968
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.88	5	161
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.606	25.738	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.175	15	245
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	3.015	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	171
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1513
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	265
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	217
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	1140
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	611
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	637
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	84
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.032	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.183	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	56
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.165	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	1.632	2.279	634
X-RAY DIFFRACTION	r_mcbond_other	1.633	2.278	633
X-RAY DIFFRACTION	r_mcangle_it	2.659	3.417	792
X-RAY DIFFRACTION	r_mcangle_other	2.657	3.419	793
X-RAY DIFFRACTION	r_scbond_it	2.309	2.649	692
X-RAY DIFFRACTION	r_scbond_other	2.32	2.618	685
X-RAY DIFFRACTION	r_scangle_it	3.639	3.851	1004
X-RAY DIFFRACTION	r_scangle_other	3.658	3.801	993
X-RAY DIFFRACTION	r_lrange_it	6.169	27.978	1401
X-RAY DIFFRACTION	r_lrange_other	6.165	27.485	1381

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 (%)
1.55-1.589	0.288	71	0.273	1566	X-RAY DIFFRACTION	99.2723
1.589-1.633	0.313	71	0.245	1543	X-RAY DIFFRACTION	99.8762
1.633-1.68	0.291	68	0.233	1487	X-RAY DIFFRACTION	100
1.68-1.732	0.295	69	0.215	1501	X-RAY DIFFRACTION	100
1.732-1.789	0.288	65	0.218	1411	X-RAY DIFFRACTION	99.8647
1.789-1.851	0.265	63	0.2	1366	X-RAY DIFFRACTION	100
1.851-1.921	0.202	60	0.19	1322	X-RAY DIFFRACTION	100
1.921-1.999	0.219	60	0.19	1305	X-RAY DIFFRACTION	100
1.999-2.088	0.273	57	0.201	1234	X-RAY DIFFRACTION	100
2.088-2.189	0.261	53	0.19	1156	X-RAY DIFFRACTION	100
2.189-2.308	0.232	52	0.197	1141	X-RAY DIFFRACTION	100
2.308-2.447	0.214	49	0.206	1070	X-RAY DIFFRACTION	100
2.447-2.615	0.286	46	0.209	998	X-RAY DIFFRACTION	100
2.615-2.824	0.22	43	0.22	932	X-RAY DIFFRACTION	100
2.824-3.092	0.32	40	0.207	885	X-RAY DIFFRACTION	100
3.092-3.455	0.206	37	0.185	788	X-RAY DIFFRACTION	100
3.455-3.985	0.22	32	0.182	698	X-RAY DIFFRACTION	100
3.985-4.869	0.184	27	0.158	608	X-RAY DIFFRACTION	99.8428
4.869-6.839	0.17	23	0.218	489	X-RAY DIFFRACTION	100
6.839-41.689	0.279	14	0.193	296	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Origin x: -12.8202 Å / Origin y: 52.1562 Å / Origin z: 15.2609 Å

	11	12	13	21	22	23	31	32	33
T	0.0758 Å²	0.032 Å²	-0.0093 Å²	-	0.0267 Å²	0.0117 Å²	-	-	0.03 Å²
L	0.2489 °²	0.3581 °²	0.0644 °²	-	0.7209 °²	0.3262 °²	-	-	0.9186 °²
S	-0.0708 Å °	-0.0298 Å °	-0.0334 Å °	-0.0946 Å °	0.0096 Å °	0.0049 Å °	-0.1226 Å °	-0.0248 Å °	0.0612 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	4 - 161
2	X-RAY DIFFRACTION	1	ALL	AAA	201

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