PDB-7q18: Beta-lactoglobulin mutant FAF (I56F/L39A/M107F), unliganded form

ID or keywords:

Entry

Database: PDB / ID: 7q18

Title

Beta-lactoglobulin mutant FAF (I56F/L39A/M107F), unliganded form

Components

Beta-lactoglobulin

Keywords

TRANSPORT PROTEIN / lactoglobulin / mutation / lipocalin

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: 1.804 Å

Authors

Loch, J.I. / Cymborowski, M.T. / Minor, W. / 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 / 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	Oct 23, 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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Download

PDBx/mmCIF format	7q18.cif.gz	128.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7q18.ent.gz		Display	PDB format
PDBx/mmJSON format	7q18.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7q18_validation.pdf.gz	442.6 KB	Display	wwPDB validaton report
Full document	7q18_full_validation.pdf.gz	443.8 KB	Display
Data in XML	7q18_validation.xml.gz	13.2 KB	Display
Data in CIF	7q18_validation.cif.gz	17.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q1/7q18 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/7q18	HTTPS FTP

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Related structure data

Related structure data	7q17C 7q19C 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

BBB: Beta-lactoglobulin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, dimer, chami AAA+BBB

Unit cell

Length a, b, c (Å)	45.905, 64.298, 55.497
Angle α, β, γ (deg.)	90.000, 112.893, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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)

#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
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.07 Å³/Da / Density % sol: 40.53 %
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

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 17, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 27108 / % possible obs: 99 % / Redundancy: 3.7 % / CC_1/2: 0.992 / R_rim(I) all: 0.059 / Net I/σ(I): 35.1
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1363 / CC_1/2: 0.884 / R_rim(I) all: 0.833 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy

Resolution: 1.804→27.733 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.953 / SU B: 9.823 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.131 / Details: Hydrogen atoms were added at riding positions

	R_factor	Num. reflection	% reflection
R_free	0.233	1074	3.965 %
R_work	0.1992	26016	-
all	0.201	-	-
obs	-	27090	98.613 %

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: 45.982 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.805 Å²	0 Å²	1.536 Å²
2-	-	0.188 Å²	0 Å²
3-	-	-	-3.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.804→27.733 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2364	0	5	71	2440

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2418
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.017	2379
X-RAY DIFFRACTION	r_angle_refined_deg	1.662	1.636	3269
X-RAY DIFFRACTION	r_angle_other_deg	1.365	1.584	5515
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.057	5	294
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.218	25.364	110
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.416	15	459
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.654	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	321
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2637
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	483
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	340
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	1974
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	1090
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	1179
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	79
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.261	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.288	0.2	83
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.211	0.2	7
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.123	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.554	2.209	1188
X-RAY DIFFRACTION	r_mcbond_other	1.553	2.209	1187
X-RAY DIFFRACTION	r_mcangle_it	2.369	3.298	1475
X-RAY DIFFRACTION	r_mcangle_other	2.369	3.298	1476
X-RAY DIFFRACTION	r_scbond_it	2.022	2.513	1230
X-RAY DIFFRACTION	r_scbond_other	2.021	2.513	1231
X-RAY DIFFRACTION	r_scangle_it	3.263	3.663	1793
X-RAY DIFFRACTION	r_scangle_other	3.262	3.663	1794
X-RAY DIFFRACTION	r_lrange_it	5.485	25.26	2387
X-RAY DIFFRACTION	r_lrange_other	5.44	25.035	2377
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.146	0.05	4227

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	0.14609	0.05008
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.14609	0.05008

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 (%)
1.804-1.851	0.269	66	0.312	1817	X-RAY DIFFRACTION	93.542
1.851-1.902	0.298	85	0.288	1859	X-RAY DIFFRACTION	99.0826
1.902-1.957	0.242	82	0.275	1788	X-RAY DIFFRACTION	99.2569
1.957-2.017	0.294	69	0.254	1807	X-RAY DIFFRACTION	99.2593
2.017-2.083	0.276	81	0.228	1739	X-RAY DIFFRACTION	99.6169
2.083-2.156	0.263	63	0.211	1649	X-RAY DIFFRACTION	99.5349
2.156-2.237	0.258	78	0.208	1599	X-RAY DIFFRACTION	99.6435
2.237-2.328	0.222	60	0.201	1551	X-RAY DIFFRACTION	99.6906
2.328-2.432	0.207	65	0.21	1493	X-RAY DIFFRACTION	99.8718
2.432-2.55	0.242	60	0.198	1446	X-RAY DIFFRACTION	99.8012
2.55-2.687	0.234	55	0.204	1347	X-RAY DIFFRACTION	99.7865
2.687-2.85	0.313	55	0.214	1289	X-RAY DIFFRACTION	100
2.85-3.046	0.291	50	0.215	1222	X-RAY DIFFRACTION	99.7647
3.046-3.289	0.251	33	0.207	1143	X-RAY DIFFRACTION	99.661
3.289-3.602	0.209	40	0.19	1026	X-RAY DIFFRACTION	99.3476
3.602-4.024	0.24	41	0.174	946	X-RAY DIFFRACTION	99.496
4.024-4.642	0.185	40	0.154	822	X-RAY DIFFRACTION	98.627
4.642-5.674	0.184	24	0.162	705	X-RAY DIFFRACTION	98.1157
5.674-7.975	0.181	19	0.204	543	X-RAY DIFFRACTION	97.4004
7.975-27.733	0.301	8	0.233	225	X-RAY DIFFRACTION	68.9349

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	4.4958	0.7627	-12.3305	0.5065	-1.9242	33.8953	0.1705	1.0172	0.141	0.4032	0.0993	0.3691	-0.3106	-2.8129	-0.2698	0.4203	0.015	0.2368	0.2843	-0.114	0.6861	-0.728	-9.2477	3.1549
2	1.075	-0.8443	-1.5352	1.7068	-0.3348	4.8584	-0.045	-0.1962	0.0249	-0.0148	0.13	-0.0031	0.0108	0.5231	-0.085	0.0921	0.0149	-0.0331	0.2752	-0.0197	0.2348	12.6479	0.4472	5.9362
3	5.8496	7.6601	8.5957	12.9343	14.237	20.4348	-0.0995	-0.2808	-0.0716	-0.3074	0.4276	-0.601	-0.0157	1.1412	-0.3281	0.1011	0.0445	-0.0109	0.453	-0.0132	0.3118	21.5332	0.1574	7.2924
4	9.673	4.764	1.3282	12.6489	4.6451	8.1387	-0.1288	0.1962	-0.4353	-0.3083	0.0721	-0.297	0.5307	0.3862	0.0567	0.2271	0.1069	0.028	0.1603	0.0527	0.1679	13.6489	-11.5085	0.602
5	24.5467	-1.3698	15.831	2.45	-10.3902	48.342	0.0909	-1.2336	-1.0653	-0.3588	-0.0295	-0.12	1.3543	-0.4463	-0.0614	0.3845	0.191	0.1407	0.2264	0.0009	0.3535	15.9898	-15.2027	9.4995
6	2.2236	-0.5517	-2.0729	1.8129	-0.019	3.4529	-0.0337	-0.0678	-0.0692	-0.0149	0.0933	0.3113	0.1185	0.0289	-0.0596	0.1363	0.0105	-0.0488	0.2342	-0.0102	0.2546	6.5251	-0.9762	3.3692
7	1.8447	0.5252	-1.2616	2.875	-0.7468	4.2726	0.0861	-0.002	0.236	0.0758	0.1679	0.327	-0.4013	0.0299	-0.254	0.1421	0.0435	0.0083	0.2247	-0.02	0.2618	4.184	6.7721	9.987
8	3.1874	0.6969	-3.5325	2.2119	0.725	5.0104	-0.0283	-0.0814	0.1618	-0.0725	0.1671	0.106	-0.0327	0.193	-0.1388	0.1413	0.0197	-0.048	0.243	-0.0037	0.2064	-4.0691	10.1712	32.5562
9	16.9926	-10.6375	-3.6034	10.4192	2.9013	2.9102	-0.272	-0.9761	0.2347	0.4612	0.5748	-0.1194	0.1948	0.862	-0.3027	0.2077	-0.0037	-0.0451	0.3947	-0.0494	0.1694	0.8943	11.5132	41.6536
10	11.1371	-4.1542	2.3363	11.2056	-3.3787	8.611	0.1617	-0.2379	0.8161	0.1541	0.0699	-0.1331	-0.6409	0.0833	-0.2316	0.1988	-0.0224	0.0791	0.1644	-0.0188	0.2735	-9.2961	23.4905	36.7614
11	21.0031	9.303	-4.4203	9.3073	9.2198	25.0329	-0.0829	-0.3428	0.0877	-0.7005	0.1931	0.032	-1.4159	0.8507	-0.1102	0.3212	-0.1566	-0.0863	0.1864	-0.0463	0.4426	0.5642	24.201	34.9733
12	2.455	-0.5547	-2.2296	2.519	0.9129	4.1255	-0.1072	0.0347	-0.0334	-0.2489	0.0828	0.1994	0.0128	-0.146	0.0244	0.1226	0.0163	-0.0576	0.2574	-0.0008	0.2404	-9.1617	9.5301	29.7605
13	10.157	4.0275	-5.9061	11.8285	-1.3617	14.8442	-0.0625	0.5643	-0.2718	-1.0256	-0.0598	0.437	0.576	-1.0466	0.1223	0.1886	-0.0156	-0.1026	0.2951	-0.0258	0.2276	-11.2775	5.3609	20.8535
14	1.6016	-0.2442	-1.6366	6.1587	-1.7403	6.0188	-0.3003	-0.2138	-0.0972	-0.2578	0.3453	0.0429	0.3822	0.0419	-0.045	0.1492	0.0359	-0.0034	0.2555	-0.0423	0.2052	-0.1927	3.5793	26.2638

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	3 - 8
2	X-RAY DIFFRACTION	2	ALL	AAA	9 - 50
3	X-RAY DIFFRACTION	3	ALL	AAA	51 - 68
4	X-RAY DIFFRACTION	4	ALL	AAA	69 - 82
5	X-RAY DIFFRACTION	5	ALL	AAA	83 - 90
6	X-RAY DIFFRACTION	6	ALL	AAA	91 - 126
7	X-RAY DIFFRACTION	7	ALL	AAA	127 - 160
8	X-RAY DIFFRACTION	8	ALL	BBB	5 - 48
9	X-RAY DIFFRACTION	9	ALL	BBB	49 - 70
10	X-RAY DIFFRACTION	10	ALL	BBB	71 - 82
11	X-RAY DIFFRACTION	11	ALL	BBB	83 - 91
12	X-RAY DIFFRACTION	12	ALL	BBB	92 - 129
13	X-RAY DIFFRACTION	13	ALL	BBB	130 - 139
14	X-RAY DIFFRACTION	14	ALL	BBB	140 - 161

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