PDB-6xk0: Albumin-dexamethasone complex

ID or keywords:

Entry

Database: PDB / ID: 6xk0

Title

Albumin-dexamethasone complex

Components

Albumin

Keywords

TRANSPORT PROTEIN / Drug transport / ESA / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space ...
Similarity search - Function

Biological species

Equus caballus (horse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Czub, M.P. / Majorek, K.A. / Shabalin, I.G. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Funding support

United States, 1items

Citation

Journal: Iucrj / Year: 2020
Title: Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy.
Authors: Shabalin, I.G. / Czub, M.P. / Majorek, K.A. / Brzezinski, D. / Grabowski, M. / Cooper, D.R. / Panasiuk, M. / Chruszcz, M. / Minor, W.

History

Deposition	Jun 24, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Aug 5, 2020	Group: Other / Structure summary / Category: audit_author / pdbx_SG_project / struct_keywords / Item: _struct_keywords.text
Revision 1.2	Nov 25, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6xk0.cif.gz	255.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6xk0.ent.gz	205.8 KB	Display	PDB format
PDBx/mmJSON format	6xk0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6xk0_validation.pdf.gz	758.9 KB	Display	wwPDB validaton report
Full document	6xk0_full_validation.pdf.gz	763.2 KB	Display
Data in XML	6xk0_validation.xml.gz	24.3 KB	Display
Data in CIF	6xk0_validation.cif.gz	34.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xk/6xk0 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/6xk0	HTTPS FTP

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Related structure data

Related structure data	3v08S S: Starting model for refinement
Similar structure data	2xvq-2 5otb-4 6r7s-d 6u4x-d 6m5d-d 2bxf-1 3lu6-2 5dqf-d 5id9-d 6mdq-d 6oci-d 4imi-1 2xvu-2 5v0v-d 4lb2-1 2vue-2 5otb-2 4g03-2 4emx-1 6u5a-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	#258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (14) #37 - Jan 2003 Serum Albumin similarity (9) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8) #143 - Nov 2011 Toll-like Receptors similarity (1) #20 - Aug 2001 Poliovirus and Rhinovirus similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (14)
#37 - Jan 2003
Serum Albumin
similarity (9)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (9)
#155 - Nov 2012
Vitamin D Receptor
similarity (8)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#20 - Aug 2001
Poliovirus and Rhinovirus
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Albumin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology, gel filtration

Unit cell

Length a, b, c (Å)	94.983, 94.983, 143.591
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

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Protein , 1 types, 1 molecules A

#1: Protein	Albumin Mass: 65784.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747

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Non-polymers , 5 types, 235 molecules

#2: Chemical	ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE Mass: 392.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₂₉FO₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#3: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#4: Chemical	ChemComp-MYR / MYRISTIC ACID Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₈O₂
#5: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 4 / Source method: obtained synthetically
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.84 Å³/Da / Density % sol: 56.73 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Prior to crystallization, 15 mg/ml protein was incubated with dexamethasone powder (10-fold molar excess) for 60 min at room temperature, and the mixture with the powder in suspension was ...Details: Prior to crystallization, 15 mg/ml protein was incubated with dexamethasone powder (10-fold molar excess) for 60 min at room temperature, and the mixture with the powder in suspension was used for crystallization. 1 ul of this mixture was mixed with 1 ul of the well condition (1.8 M ammonium dihydrogen citrate, pH 7.0) and equilibrated against the well solution in 15-Well hanging drop crystallization plate (Qiagen, EasyXtal). 1:1 mixture of Paratone N and mineral oil was used as a cryoprotectant

Crystal

Density Matthews: 2.84 Å³/Da / Density % sol: 56.73 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Prior to crystallization, 15 mg/ml protein was incubated with dexamethasone powder (10-fold molar excess) for 60 min at room temperature, and the mixture with the powder in suspension was ...

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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: 0.979 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 28870 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / B_iso Wilson estimate: 40 Å² / R_merge(I) obs: 0.11 / R_pim(I) all: 0.055 / R_rim(I) all: 0.123 / Χ²: 0.886 / Net I/av σ(I): 15.3 / Net I/σ(I): 8.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.4-2.44	3.5	1.053	1412	0.619	0.605	1.221	0.911	98.3
2.44-2.49	3.9	1.036	1416	0.638	0.572	1.189	0.935	99.4
2.49-2.53	4.2	1.021	1432	0.752	0.546	1.161	0.908	99.7
2.53-2.59	4.5	0.942	1440	0.818	0.49	1.064	0.938	99.8
2.59-2.64	4.9	0.882	1448	0.845	0.443	0.988	0.911	99.7
2.64-2.7	5	0.817	1442	0.856	0.403	0.912	0.928	99.8
2.7-2.77	5.1	0.718	1435	0.904	0.35	0.8	0.91	99.7
2.77-2.85	5.2	0.566	1429	0.92	0.276	0.631	0.922	99.9
2.85-2.93	5.2	0.44	1447	0.95	0.214	0.49	0.924	99.9
2.93-3.02	5.2	0.318	1441	0.967	0.155	0.354	0.93	99.9
3.02-3.13	5.2	0.239	1445	0.98	0.116	0.266	0.934	99.9
3.13-3.26	5.2	0.169	1445	0.986	0.082	0.189	0.9	99.9
3.26-3.41	5.2	0.13	1456	0.991	0.063	0.144	0.883	99.9
3.41-3.58	5.2	0.094	1430	0.991	0.045	0.104	0.816	99.9
3.58-3.81	5.2	0.075	1456	0.994	0.036	0.083	0.757	99.9
3.81-4.1	5.2	0.067	1445	0.993	0.032	0.075	0.8	100
4.1-4.52	5.2	0.074	1450	0.991	0.036	0.082	1.091	100
4.52-5.17	5.1	0.078	1451	0.99	0.038	0.087	1.247	100
5.17-6.51	5.1	0.051	1452	0.993	0.025	0.057	0.598	100
6.51-50	4.9	0.054	1498	0.983	0.027	0.06	0.507	99.8

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Processing

Software

Name	Version	Classification
HKL-3000		data scaling
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
MOLREP		phasing
SCALEPACK		data scaling
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3V08

3v08

Resolution: 2.4→47.54 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.9 / SU B: 20.237 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.634 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2492	1132	4.7 %	RANDOM
R_work	0.2033	-	-	-
obs	0.2054	22871	83.67 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 166.13 Å² / B_iso mean: 56.799 Å² / B_iso min: 15.75 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	-0.02 Å²	-0 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: final / Resolution: 2.4→47.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4589	0	61	228	4878
B_iso mean	-	-	73.86	39.02	-
Num. residues	-	-	-	-	581

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	4761
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	4419
X-RAY DIFFRACTION	r_angle_refined_deg	1.127	1.647	6444
X-RAY DIFFRACTION	r_angle_other_deg	1.148	1.591	10344
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.967	5	580
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.544	23.574	235
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.695	15	853
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.818	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.041	0.2	611
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	5251
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	920

LS refinement shell

Resolution: 2.4→2.462 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.309	23	-
R_work	0.259	594	-
all	-	617	-
obs	-	-	29.2 %

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	2.8048	0.8563	3.4497	4.5941	2.5512	9.1518	0.0118	-0.0779	0.4452	-0.0495	-0.13	-0.3529	-0.4746	0.1405	0.1182	0.3177	-0.1256	-0.0369	0.1178	0.0594	0.2015	49.899	37.698	76.084
2	2.5967	-0.1037	-0.5679	3.617	5.5324	12.2854	0.0265	0.0336	0.4419	-0.6887	-0.0719	-0.1693	-1.2899	0.0854	0.0454	0.6793	-0.0699	-0.0446	0.1868	0.1228	0.4038	48.707	45.226	72.507
3	2.1211	-1.7043	-0.2976	6.5002	0.2562	4.7554	0.1921	0.2189	0.3661	-0.2329	-0.0907	0.0202	-0.6177	-0.3728	-0.1013	0.4822	0.0372	-0.0661	0.2663	0.0463	0.1715	35.38	37.439	66.227
4	2.531	-1.6697	4.7511	2.2401	-3.604	9.1963	0.1432	0.5594	0.8525	-0.1194	-1.1241	0.4247	0.0617	1.2335	0.9809	0.9711	0.0073	0.5653	1.1717	-0.1291	1.682	61.735	25.965	56.183
5	6.3173	-3.7969	-0.879	6.2566	2.3216	3.9066	0.1288	0.6111	0.3136	-0.8618	0.1477	-1.3788	-0.1595	0.9209	-0.2765	0.4752	-0.1428	0.1972	0.3826	-0.0233	0.4177	57.019	21.955	64.861
6	2.824	2.3657	1.0549	4.3978	1.5087	3.5985	0.1297	-0.2083	0.0198	0.2293	-0.1174	-0.1449	-0.0379	0.1737	-0.0123	0.1288	-0.0575	-0.0372	0.071	0.0044	0.0191	46.799	20.401	85.31
7	1.3018	1.9001	-1.225	5.4724	-1.2392	7.7093	0.0704	-0.1427	-0.1379	0.702	-0.2717	-0.0026	0.5424	-0.7532	0.2013	0.5848	-0.0753	-0.1318	0.3264	0.0268	0.1038	38.887	7.077	98.392
8	2.4681	-0.3531	0.0377	3.6995	0.1557	5.9483	0.2438	-0.3955	-0.4864	0.5514	-0.4213	0.3751	0.7251	-0.9573	0.1776	0.4251	-0.2753	-0.0554	0.3046	0.0342	0.154	31.998	1.818	90.738
9	6.627	-1.9062	4.5045	5.5677	-0.5077	5.9334	-0.0054	0.1047	-0.403	0.2748	0.2184	-0.4527	0.2047	0.3799	-0.2131	0.1564	-0.0291	0.0225	0.0944	-0.0532	0.1187	38.728	2.41	62.372
10	5.2969	2.5228	2.7121	2.5229	1.7582	6.071	-0.0217	-0.1727	-0.0315	-0.0014	-0.1591	0.4047	0.0413	-0.5887	0.1808	0.1153	0.0042	-0.0241	0.0726	-0.0312	0.1407	29.151	8.531	68.021
11	3.9859	0.1224	-2.9281	3.9171	-1.7374	4.789	0.1145	0.1498	-0.1382	-0.6309	-0.2082	-0.1643	0.1489	-0.0802	0.0938	0.2518	-0.0086	0.0349	0.0923	-0.0451	0.0539	37.505	3.996	44.52
12	3.8586	3.8815	-1.9396	17.3881	-8.6535	4.3078	0.0131	0.1588	-0.4438	-0.9557	-0.188	-0.328	0.4761	0.0821	0.1749	0.4584	0.0063	-0.1281	0.342	-0.1673	0.2012	30.122	-1.921	38.619

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 32
2	X-RAY DIFFRACTION	2	A	33 - 67
3	X-RAY DIFFRACTION	3	A	68 - 113
4	X-RAY DIFFRACTION	4	A	114 - 131
5	X-RAY DIFFRACTION	5	A	132 - 187
6	X-RAY DIFFRACTION	6	A	188 - 288
7	X-RAY DIFFRACTION	7	A	289 - 324
8	X-RAY DIFFRACTION	8	A	325 - 390
9	X-RAY DIFFRACTION	9	A	391 - 440
10	X-RAY DIFFRACTION	10	A	441 - 502
11	X-RAY DIFFRACTION	11	A	503 - 568
12	X-RAY DIFFRACTION	12	A	569 - 583

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