PDB-7kot: Energetic and structural effects of the Tanford transition on the...

ID or keywords:

Entry

Database: PDB / ID: 7kot

Title

Energetic and structural effects of the Tanford transition on the ligand recognition of bovine Beta-lactoglobulin

Components

Beta-lactoglobulin

Keywords

TRANSPORT PROTEIN / Bovine beta-lactoglobulin / Lipocalin / Tanford transition / Structural energetics

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: 1.74 Å

Authors

Rodriguez-Hernandez, A. / Rodriguez-Romero, A.

Funding support

Mexico, 1items

Citation

Journal: Arch.Biochem.Biophys. / Year: 2021
Title: Energetic and structural effects of the Tanford transition on ligand recognition of bovine beta-lactoglobulin.
Authors: Labra-Nunez, A. / Cofas-Vargas, L.F. / Gutierrez-Magdaleno, G. / Gomez-Velasco, H. / Rodriguez-Hernandez, A. / Rodriguez-Romero, A. / Garcia-Hernandez, E.

History

Deposition	Nov 9, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 20, 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	7kot.cif.gz	75.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7kot_validation.pdf.gz	586.9 KB	Display	wwPDB validaton report
Full document	7kot_full_validation.pdf.gz	586.9 KB	Display
Data in XML	7kot_validation.xml.gz	9.5 KB	Display
Data in CIF	7kot_validation.cif.gz	12.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/7kot ftp://data.pdbj.org/pub/pdb/validation_reports/ko/7kot	HTTPS FTP

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Related structure data

Related structure data	7kp5C 1bebS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4y0r-d 1b0o-d 4ib9-d 4gny-d 4y0s-d 4kii-d 3blg-d 3uex-d 3uew-d 4dq3-d 6rwq-d 6rwr-d 6ge7-d 5htd-d 6gf9-d 4ib8-d 1gx9-d 1bso-d 4y0p-d 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

A: Beta-lactoglobulin

hetero molecules

18.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.652, 53.652, 112.021
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: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02754
#2: Chemical	ChemComp-SDS / DODECYL SULFATE Mass: 266.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₄S / Comment: detergent*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.54 Å³/Da / Density % sol: 51.63 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M NaCl, pH 4.5 and in 0.05 M Tris-HCl, 0.1 M NaCl, pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 16, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.74→46.46 Å / Num. obs: 19905 / % possible obs: 99.6 % / Redundancy: 14.1 % / CC_1/2: 0.89 / Net I/σ(I): 83.2
Reflection shell	Resolution: 1.74→1.77 Å / Num. unique obs: 978 / CC_1/2: 0.89

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BEB

1beb

Resolution: 1.74→46.46 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.95 / SU B: 4.809 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2286	1012	5.114 %
R_work	0.1931	18776	-
all	0.195	-	-
obs	-	19788	99.592 %

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: 32.581 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.47 Å²	0.235 Å²	0 Å²
2-	-	0.47 Å²	-0 Å²
3-	-	-	-1.526 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→46.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1221	0	17	115	1353

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.013	1258
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1224
X-RAY DIFFRACTION	r_angle_refined_deg	2.222	1.655	1698
X-RAY DIFFRACTION	r_angle_other_deg	1.497	1.609	2856
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.571	5	155
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.957	25.385	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.923	15	236
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	5.129	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	169
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	1346
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	215
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	191
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	1122
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	601
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	687
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	83
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.21	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	18
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.114	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.358	2.396	626
X-RAY DIFFRACTION	r_mcbond_other	2.359	2.395	625
X-RAY DIFFRACTION	r_mcangle_it	3.538	3.574	779
X-RAY DIFFRACTION	r_mcangle_other	3.536	3.575	780
X-RAY DIFFRACTION	r_scbond_it	3.097	2.703	632
X-RAY DIFFRACTION	r_scbond_other	3.095	2.703	633
X-RAY DIFFRACTION	r_scangle_it	4.804	3.896	919
X-RAY DIFFRACTION	r_scangle_other	4.801	3.896	920
X-RAY DIFFRACTION	r_lrange_it	6.645	28.28	1314
X-RAY DIFFRACTION	r_lrange_other	6.608	27.807	1295

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
1.74-1.785	0.326	74	0.267	1378	0.27	1457	0.842	0.869	99.6568	0.232
1.785-1.834	0.283	81	0.233	1292	0.236	1376	0.882	0.909	99.782	0.199
1.834-1.887	0.272	83	0.24	1275	0.242	1372	0.913	0.914	98.9796	0.194
1.887-1.945	0.226	69	0.212	1272	0.212	1343	0.933	0.934	99.8511	0.182
1.945-2.008	0.284	62	0.189	1210	0.193	1277	0.916	0.946	99.6085	0.157
2.008-2.079	0.228	76	0.187	1181	0.189	1258	0.933	0.949	99.9205	0.163
2.079-2.157	0.265	65	0.191	1141	0.195	1209	0.926	0.947	99.7519	0.161
2.157-2.245	0.225	68	0.189	1076	0.192	1158	0.939	0.951	98.791	0.159
2.245-2.344	0.217	54	0.189	1059	0.19	1125	0.941	0.951	98.9333	0.167
2.344-2.458	0.326	50	0.199	1006	0.204	1065	0.892	0.943	99.1549	0.175
2.458-2.591	0.241	36	0.203	989	0.204	1028	0.921	0.943	99.7082	0.185
2.591-2.748	0.289	39	0.208	916	0.211	960	0.912	0.942	99.4792	0.198
2.748-2.937	0.247	46	0.2	877	0.202	924	0.919	0.943	99.8918	0.198
2.937-3.171	0.193	42	0.203	826	0.203	870	0.957	0.943	99.7701	0.211
3.171-3.472	0.257	28	0.188	760	0.19	788	0.927	0.951	100	0.205
3.472-3.879	0.188	46	0.171	684	0.172	730	0.964	0.966	100	0.196
3.879-4.474	0.184	30	0.166	619	0.167	649	0.962	0.973	100	0.205
4.474-5.467	0.245	30	0.155	522	0.159	552	0.952	0.977	100	0.2
5.467-7.678	0.256	19	0.22	433	0.221	452	0.928	0.949	100	0.275
7.678-46.464	0.116	14	0.23	260	0.225	276	0.973	0.949	99.2754	0.321

Refinement TLS params.

Method: refined / Origin x: 15.8026 Å / Origin y: -4.4215 Å / Origin z: 3.458 Å

	11	12	13	21	22	23	31	32	33
T	0.1133 Å²	-0.0481 Å²	0.0167 Å²	-	0.0394 Å²	-0.0157 Å²	-	-	0.0204 Å²
L	0.6071 °²	0.2052 °²	-0.3068 °²	-	1.0399 °²	-0.5161 °²	-	-	2.3352 °²
S	-0.1556 Å °	0.0858 Å °	-0.0098 Å °	-0.102 Å °	0.0577 Å °	-0.0599 Å °	-0.0193 Å °	-0.194 Å °	0.0979 Å °

Refinement TLS group

Selection: ALL

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