PDB-7q2n: Beta-lactoglobulin mutant FAF (I56F/L39A/M107F) in complex with d...

ID or keywords:

Entry

Database: PDB / ID: 7q2n

Title

Beta-lactoglobulin mutant FAF (I56F/L39A/M107F) in complex with desipramine (FAF-DSM)

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: 1.7 Å

Authors

Loch, J.I. / Barciszewski, J. / 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 25, 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 / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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	7q2n.cif.gz	139.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7q2n.ent.gz		Display	PDB format
PDBx/mmJSON format	7q2n.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q2/7q2n ftp://data.pdbj.org/pub/pdb/validation_reports/q2/7q2n	HTTPS FTP

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Related structure data

Related structure data	7q17C 7q18C 7q19C 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

BBB: Beta-lactoglobulin

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	55.821, 73.340, 179.701
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	AAA-358- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: CYS / End label comp-ID: CYS / Auth seq-ID: 5 - 160 / Label seq-ID: 5 - 160

Dom-ID	Component-ID	Auth asym-ID	Label asym-ID
1	1	AAA	A
2	2	BBB	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AAABBB

#1: Protein	Beta-lactoglobulin / Beta-LG Mass: 18240.930 Da / Num. of mol.: 2 / Mutation: L1A, I2S, L39A, I56F, M107F 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: 18240.930 Da / Num. of mol.: 2 / Mutation: L1A, I2S, L39A, I56F, M107F
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 , 6 types, 155 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.: 4 / Source method: obtained synthetically / Formula: C₁₈H₂₂N₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant, inhibitor*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.52 Å³/Da / Density % sol: 51.2 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.7→46.38 Å / Num. obs: 41144 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC_1/2: 1 / R_rim(I) all: 0.069 / Net I/σ(I): 17.97
Reflection shell	Resolution: 1.7→1.8 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 6512 / CC_1/2: 0.903 / R_rim(I) all: 1.351

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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: 1.7→46.38 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.964 / SU B: 12.805 / SU ML: 0.157 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.105 / Details: Hydrogen atoms were added at riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2328	1042	2.537 %
R_work	0.2032	40027	-
all	0.204	-	-
obs	-	41069	99.934 %

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: 44.931 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.806 Å²	-0 Å²	-0 Å²
2-	-	7.96 Å²	-0 Å²
3-	-	-	-3.154 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→46.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2493	0	101	146	2740

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	2658
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2577
X-RAY DIFFRACTION	r_angle_refined_deg	1.599	1.643	3595
X-RAY DIFFRACTION	r_angle_other_deg	1.384	1.629	5974
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.423	5	316
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.445	25.667	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.151	15	481
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.053	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	340
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3145
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	543
X-RAY DIFFRACTION	r_nbd_refined	0.177	0.2	414
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	2288
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	1232
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	1250
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.2	0.2	113
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.153	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	78
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.212	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	2.534	3.812	1261
X-RAY DIFFRACTION	r_mcbond_other	2.529	3.81	1260
X-RAY DIFFRACTION	r_mcangle_it	4.028	5.697	1572
X-RAY DIFFRACTION	r_mcangle_other	4.029	5.7	1573
X-RAY DIFFRACTION	r_scbond_it	3.412	4.369	1397
X-RAY DIFFRACTION	r_scbond_other	3.411	4.362	1390
X-RAY DIFFRACTION	r_scangle_it	5.555	6.345	2021
X-RAY DIFFRACTION	r_scangle_other	5.565	6.333	2010
X-RAY DIFFRACTION	r_lrange_it	7.496	44.881	2696
X-RAY DIFFRACTION	r_lrange_other	7.483	44.836	2690
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.158	0.05	4320

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.15827	0.05007
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.15827	0.05007

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
1.7-1.744	0.415	74	0.396	2951	0.396	3027	0.248	0.236	99.9339	0.336
1.744-1.792	0.412	75	0.397	2815	0.398	2894	0.178	0.196	99.8618	0.331
1.792-1.844	0.331	68	0.363	2764	0.362	2834	0.163	0.137	99.9294	0.293
1.844-1.9	0.314	60	0.336	2685	0.336	2746	0.188	0.192	99.9636	0.273
1.9-1.963	0.307	58	0.306	2635	0.306	2694	0.41	0.404	99.9629	0.25
1.963-2.031	0.261	63	0.279	2513	0.278	2580	0.496	0.527	99.845	0.234
2.031-2.108	0.295	54	0.27	2460	0.27	2514	0.592	0.552	100	0.226
2.108-2.194	0.276	76	0.253	2347	0.253	2423	0.703	0.662	100	0.22
2.194-2.291	0.278	67	0.235	2259	0.237	2326	0.78	0.796	100	0.208
2.291-2.403	0.329	56	0.223	2152	0.225	2210	0.806	0.864	99.9095	0.198
2.403-2.532	0.19	65	0.214	2073	0.213	2138	0.92	0.906	100	0.19
2.532-2.685	0.26	69	0.218	1921	0.219	1991	0.905	0.926	99.9498	0.201
2.685-2.87	0.297	50	0.194	1836	0.196	1888	0.902	0.935	99.8941	0.183
2.87-3.099	0.287	50	0.185	1722	0.188	1772	0.917	0.944	100	0.18
3.099-3.393	0.194	43	0.179	1593	0.179	1637	0.95	0.957	99.9389	0.18
3.393-3.791	0.196	39	0.159	1448	0.16	1487	0.959	0.969	100	0.164
3.791-4.373	0.174	33	0.145	1296	0.146	1331	0.963	0.974	99.8497	0.158
4.373-5.344	0.122	19	0.132	1120	0.132	1139	0.976	0.98	100	0.153
5.344-7.507	0.289	16	0.204	881	0.205	897	0.936	0.956	100	0.226
7.507-46.384	0.069	7	0.166	545	0.164	552	0.994	0.965	100	0.2

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.3487	0.033	0.1335	0.1485	0.1752	0.3978	0.0154	0.0808	-0.1092	0.0173	-0.003	-0.0059	-0.0241	-0.0197	-0.0125	0.0529	0.0063	-0.0081	0.0453	-0.0412	0.0414	17.0924	-0.1514	62.0919
2	1.3175	-0.1823	0.0061	0.1532	0.3686	1.1507	-0.0242	-0.0153	-0.0571	-0.0098	0.0067	0.0215	0	0.0531	0.0176	0.0552	0.0078	-0.0135	0.0182	-0.0102	0.0282	45.0761	3.615	74.9238

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	4 - 162
2	X-RAY DIFFRACTION	1	ALL	AaA	201
3	X-RAY DIFFRACTION	1	ALL	AbA	301
4	X-RAY DIFFRACTION	1	ALL	AcA	163
5	X-RAY DIFFRACTION	1	ALL	AdA	164
6	X-RAY DIFFRACTION	1	ALL	AeA	165
7	X-RAY DIFFRACTION	1	ALL	AfA	166
8	X-RAY DIFFRACTION	1	ALL	AgA	167
9	X-RAY DIFFRACTION	1	ALL	AhA	170 - 260
10	X-RAY DIFFRACTION	2	ALL	BBB	5 - 161
11	X-RAY DIFFRACTION	2	ALL	BaB	165 - 248

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