PDB-7q2o: Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with d...

ID or keywords:

Entry

Database: PDB / ID: 7q2o

Title

Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#1)

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: 1.8 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 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7q2o.cif.gz	138.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7q2o.ent.gz		Display	PDB format
PDBx/mmJSON format	7q2o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q2/7q2o ftp://data.pdbj.org/pub/pdb/validation_reports/q2/7q2o	HTTPS FTP

-
Related structure data

Related structure data	7q17C 7q18C 7q19C 7q2nC 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

-
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)	55.667, 70.145, 179.018
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁

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: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 9 - 161 / Label seq-ID: 9 - 161

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)

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein	Beta-lactoglobulin / Beta-LG Mass: 18279.965 Da / Num. of mol.: 2 / 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 (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754

#1: Protein

Beta-lactoglobulin / Beta-LG

Mass: 18279.965 Da / Num. of mol.: 2 / 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 (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754

-
Non-polymers , 5 types, 162 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: 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
#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.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.20 M (NH4)2SO4, 0.5 M Tris-HCl pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 6, 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: 1.8→45.45 Å / Num. obs: 32842 / % possible obs: 99.2 % / Redundancy: 5.52 % / CC_1/2: 0.999 / R_rim(I) all: 0.074 / Net I/σ(I): 14.42
Reflection shell	Resolution: 1.8→1.91 Å / Num. unique obs: 5196 / CC_1/2: 0.851 / R_rim(I) all: 1.191

-
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: 1.8→45.45 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.965 / SU B: 11.364 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.117 / Details: Hydrogen atoms were added at riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2206	1000	3.045 %
R_work	0.1829	31839	-
all	0.184	-	-
obs	-	32839	99.229 %

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: 44.116 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.279 Å²	0 Å²	-0 Å²
2-	-	4.523 Å²	-0 Å²
3-	-	-	-2.244 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→45.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2443	0	94	154	2691

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2600
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	2533
X-RAY DIFFRACTION	r_angle_refined_deg	1.68	1.643	3516
X-RAY DIFFRACTION	r_angle_other_deg	1.452	1.631	5869
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.867	5	307
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.381	25.478	115
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.803	15	468
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.852	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	332
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3071
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	533
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	384
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	2232
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	1187
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1211
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	136
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.006	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.246	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.252	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.129	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	9.255	3.235	1231
X-RAY DIFFRACTION	r_mcbond_other	9.244	3.234	1230
X-RAY DIFFRACTION	r_mcangle_it	9.729	4.793	1531
X-RAY DIFFRACTION	r_mcangle_other	9.73	4.796	1532
X-RAY DIFFRACTION	r_scbond_it	15.684	4.254	1369
X-RAY DIFFRACTION	r_scbond_other	15.678	4.253	1370
X-RAY DIFFRACTION	r_scangle_it	17.498	5.926	1983
X-RAY DIFFRACTION	r_scangle_other	17.494	5.927	1984
X-RAY DIFFRACTION	r_lrange_it	18.452	39.473	2659
X-RAY DIFFRACTION	r_lrange_other	18.511	39.433	2654
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.158	0.05	4273

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	0.15845	0.05007
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.15845	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
1.798-1.845	0.432	71	0.394	2260	0.395	2388	0.287	0.324	97.6131	0.373
1.845-1.895	0.456	71	0.336	2274	0.339	2350	0.404	0.478	99.7872	0.307
1.895-1.95	0.377	69	0.315	2207	0.317	2289	0.475	0.568	99.4321	0.273
1.95-2.01	0.314	67	0.281	2123	0.282	2211	0.649	0.643	99.0502	0.237
2.01-2.076	0.317	66	0.256	2087	0.258	2165	0.71	0.754	99.4457	0.219
2.076-2.148	0.276	63	0.214	2012	0.216	2085	0.751	0.837	99.5204	0.178
2.148-2.229	0.248	61	0.196	1965	0.197	2036	0.849	0.887	99.5088	0.165
2.229-2.32	0.242	60	0.187	1881	0.188	1948	0.916	0.921	99.6407	0.155
2.32-2.423	0.235	56	0.174	1801	0.176	1862	0.921	0.93	99.7315	0.148
2.423-2.541	0.228	54	0.166	1719	0.168	1780	0.927	0.942	99.6067	0.142
2.541-2.678	0.278	52	0.173	1645	0.176	1704	0.924	0.943	99.5892	0.15
2.678-2.84	0.318	49	0.172	1558	0.176	1618	0.908	0.941	99.3202	0.15
2.84-3.035	0.207	46	0.168	1474	0.17	1531	0.944	0.948	99.2815	0.152
3.035-3.277	0.191	43	0.177	1376	0.177	1424	0.95	0.951	99.6489	0.167
3.277-3.588	0.21	40	0.163	1271	0.164	1323	0.952	0.965	99.093	0.159
3.588-4.008	0.193	36	0.156	1157	0.157	1205	0.96	0.971	99.0042	0.155
4.008-4.622	0.129	33	0.116	1028	0.116	1069	0.978	0.983	99.2516	0.124
4.622-5.646	0.14	27	0.133	874	0.133	917	0.988	0.981	98.2552	0.149
5.646-7.924	0.243	22	0.213	708	0.214	735	0.935	0.955	99.3197	0.225
7.924-45.451	0.178	14	0.216	418	0.215	448	0.824	0.954	96.4286	0.278

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	1.1627	-0.0803	-0.3267	0.1393	0.0916	0.3021	0.0035	0.0429	-0.1181	-0.0108	0.0311	0.0388	-0.0191	0.0295	-0.0346	0.0085	0.0149	-0.0083	0.0905	-0.0333	0.0803	16.5007	-0.8289	61.8578
2	0.9981	-0.0738	-0.0379	0.1953	0.3644	0.7427	0.0283	-0.0406	-0.0744	-0.0283	-0.0395	-0.0092	-0.0507	-0.0206	0.0112	0.007	0.0131	-0.0103	0.1011	0.0133	0.0743	45.1133	3.025	74.2385

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	163
3	X-RAY DIFFRACTION	1	ALL	AbA	165
4	X-RAY DIFFRACTION	1	ALL	AcA	166
5	X-RAY DIFFRACTION	1	ALL	AdA	168
6	X-RAY DIFFRACTION	1	ALL	AeA	701
7	X-RAY DIFFRACTION	1	ALL	AfA	801
8	X-RAY DIFFRACTION	1	ALL	AgA	802 - 916
9	X-RAY DIFFRACTION	2	ALL	BBB	9 - 162
10	X-RAY DIFFRACTION	2	ALL	BaB	301
11	X-RAY DIFFRACTION	2	ALL	BbB	401
12	X-RAY DIFFRACTION	2	ALL	BcB	502 - 594

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AAABBB

-
Non-polymers , 5 types, 162 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AAABBB

-Non-polymers , 5 types, 162 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AAABBB

-
Non-polymers , 5 types, 162 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi