PDB-5id9: Crystal structure of equine serum albumin in complex with phospho...

ID or keywords:

Entry

Database: PDB / ID: 5id9

Title

Crystal structure of equine serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cPA)

Components

Serum albumin

Keywords

TRANSPORT PROTEIN / Helical / Three-domain protein / Serum Albumin / Drugs delivery / cyclic phosphatidic acid / lysophospholipid

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 / lipid binding / protein-containing complex / DNA binding ...
Similarity search - Function

Biological species

Equus caballus (horse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Sekula, B. / Bujacz, A. / Rytczak, P. / Bujacz, G.

Funding support

Poland, 3items

Organization	Grant number	Country
Polish Ministry of Science and Higher Education	N N405 3639 39	Poland
National Science Centre Poland	2013/11/B/ST5/02271	Poland
National Science Centre Poland	2014/12/T/ST5/00136	Poland

Citation

Journal: Biosci.Rep. / Year: 2016
Title: Structural evidence of the species-dependent albumin binding of the modified cyclic phosphatidic acid with cytotoxic properties.
Authors: Sekula, B. / Ciesielska, A. / Rytczak, P. / Koziokiewicz, M. / Bujacz, A.

History

Deposition	Feb 24, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	May 11, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 15, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	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 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5id9.cif.gz	242.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5id9.ent.gz	197.8 KB	Display	PDB format
PDBx/mmJSON format	5id9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/id/5id9 ftp://data.pdbj.org/pub/pdb/validation_reports/id/5id9	HTTPS FTP

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Related structure data

Related structure data	5id7C 4ot2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6u5a-d 6oci-d 5iih-d 2xvq-2 6mdq-d 4zbr-d 6xk0-d 5dqf-d 2bx8-1 6m5d-d 3lu8-2 2bx8-2 6u4r-d 4lb2-1 2vue-2 3v03-1 6rjv-2 5v0v-d 3lu6-2 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 (10) #37 - Jan 2003 Serum Albumin similarity (10) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8)

Deposited unit

A: Serum albumin

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	93.860, 93.860, 141.790
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Serum albumin Mass: 65625.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue: blood / References: UniProt: F7BAY6, UniProt: P35747*PLUS
#2: Chemical	ChemComp-6A4 / (4S)-2-sulfanylidene-4-[(tetradecanoyloxy)methyl]-1,3,2lambda~5~-dioxaphospholane-2-thiolate Mass: 395.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₃₂O₄PS₂
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H₂O
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: 2.75 Å³/Da / Density % sol: 55.23 % / Description: hexagonal prism
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.8 M Ammonium sulfate, 0.1 M acetate buffer pH 4.5, cocrystallization

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 12, 2013
Radiation	Monochromator: Si (111), Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.48→50 Å / Num. obs: 24973 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / B_iso Wilson estimate: 53.1 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.088 / Net I/σ(I): 14.5
Reflection shell	Resolution: 2.48→2.58 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.991 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
REFMAC	5.8.0135	phasing
XDS	VERSION July 4, 2012	data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4OT2

4ot2

Resolution: 2.48→50 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.931 / SU B: 19.01 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22906	1012	4.1 %	RANDOM
R_work	0.17031	-	-	-
obs	0.17261	23957	99.6 %	-

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 mean: 55.701 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.6 Å²	0.3 Å²	0 Å²
2-	-	0.6 Å²	-0 Å²
3-	-	-	-1.94 Å²

Refinement step

Cycle: LAST / Resolution: 2.48→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4568	0	57	99	4724

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.019	4740
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4480
X-RAY DIFFRACTION	r_angle_refined_deg	1.847	1.928	6397
X-RAY DIFFRACTION	r_angle_other_deg	1.038	2.992	10431
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.402	5	581
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.65	24.977	213
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.395	15	849
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.671	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	697
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	5260
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	990
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.317	3.668	2321
X-RAY DIFFRACTION	r_mcbond_other	2.318	3.67	2322
X-RAY DIFFRACTION	r_mcangle_it	3.719	5.496	2900
X-RAY DIFFRACTION	r_mcangle_other	3.719	5.497	2901
X-RAY DIFFRACTION	r_scbond_it	2.999	4.132	2419
X-RAY DIFFRACTION	r_scbond_other	2.987	4.123	2409
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.929	6.016	3497
X-RAY DIFFRACTION	r_long_range_B_refined	8.1	29.018	5390
X-RAY DIFFRACTION	r_long_range_B_other	8.096	28.949	5367
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.48→2.544 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.341	68	-
R_work	0.313	1769	-
obs	-	-	99.46 %

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	1.9119	0.5153	0.1161	1.8946	0.9609	0.511	0.0119	0.0362	0.1225	-0.1606	0.0437	-0.0166	-0.0867	-0.0265	-0.0557	0.1551	-0.0652	-0.014	0.2268	0.1479	0.1233	41.1556	42.536	70.4598
2	4.1662	-1.3319	-1.6963	0.9053	0.4094	0.7325	-0.0061	-0.0095	0.1257	-0.335	0.1143	0.07	0.0636	-0.0074	-0.1082	0.3492	-0.2253	-0.0429	0.2222	0.0251	0.0721	49.518	29.5803	57.0402
3	4.4985	0.7926	-3.0799	1.0793	0.047	2.6966	-0.1596	-0.1061	-0.1559	-0.2379	0.2231	-0.0581	0.0276	0.1465	-0.0636	0.1498	-0.0712	0.023	0.169	0.0097	0.1543	53.7177	21.8355	63.1435
4	0.6345	0.8298	0.205	2.4119	-0.5765	0.6334	0.0492	0.0305	0.1675	0.2456	-0.1118	0.1037	-0.0209	0.0739	0.0627	0.191	-0.0246	-0.0627	0.1355	0.0397	0.1672	41.0306	19.6553	84.308
5	1.7587	-0.109	0.2112	3.3757	-0.6191	1.1797	-0.1549	0.0177	0.1677	0.058	0.1744	-0.2773	0.0257	0.239	-0.0195	0.0932	-0.0411	-0.0584	0.1981	0.0117	0.1602	55.3003	20.8647	83.4439
6	4.1326	1.3054	0.1275	0.7116	-0.1719	0.1605	0.3107	-0.3256	-0.0812	0.3204	-0.3129	-0.0537	-0.1777	0.1148	0.0022	0.3629	-0.0877	-0.0142	0.193	0.0306	0.0051	37.3057	5.2862	97.1271
7	2.8596	0.1488	-0.5785	1.4793	-1.7959	2.2392	0.0859	0.1322	-0.0783	0.2496	0.0934	0.1488	-0.3241	-0.1163	-0.1793	0.242	0.0178	0.0213	0.1352	-0.0043	0.145	30.4379	3.2648	89.4296
8	1.4967	-0.2207	-3.0464	0.1211	0.0942	7.7107	-0.0751	0.0742	-0.0889	0.0145	-0.0455	0.0174	0.1238	-0.113	0.1206	0.1898	-0.0152	0.0131	0.1471	-0.0069	0.1734	35.4759	-4.8915	77.3747
9	4.4058	-3.5316	-0.4485	3.4299	0.7168	0.338	0.3657	-0.198	-0.2562	-0.3927	-0.2054	0.0313	-0.1944	-0.1373	-0.1603	0.2438	0.0054	0.0408	0.2694	0.0381	0.1676	32.4784	3.0395	57.0596
10	0.9693	-0.977	0.4207	1.0955	-0.1373	0.9705	0.0698	-0.0311	0.1546	-0.0828	-0.0208	-0.1967	0.04	-0.0427	-0.049	0.2033	0.0176	-0.0182	0.1653	0.0453	0.1673	37.9842	8.976	64.9136
11	2.1515	-0.5518	1.0137	1.1064	1.6982	4.4778	0.1559	-0.0921	-0.106	0.0691	-0.1688	0.0914	0.2633	-0.3952	0.0129	0.1449	-0.0615	0.0382	0.1864	-0.0176	0.1998	23.6842	7.3898	67.4215
12	2.4962	0.268	-1.9877	0.1538	0.0027	3.2479	0.1177	-0.154	-0.0645	-0.1984	-0.0731	0.015	-0.3104	-0.0095	-0.0446	0.4017	0.0866	-0.0239	0.0691	0.0041	0.0629	32.5019	7.1069	44.1259
13	0.4201	0.0968	-0.7921	1.0229	0.2502	1.7315	-0.0373	0.0032	-0.0508	-0.2408	0.0283	-0.148	0.0013	-0.0685	0.009	0.2998	0.0202	-0.0028	0.1302	0.0141	0.0931	34.2951	-0.8377	38.25

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 106
2	X-RAY DIFFRACTION	2	A	107 - 147
3	X-RAY DIFFRACTION	3	A	148 - 198
4	X-RAY DIFFRACTION	4	A	199 - 250
5	X-RAY DIFFRACTION	5	A	251 - 295
6	X-RAY DIFFRACTION	6	A	296 - 336
7	X-RAY DIFFRACTION	7	A	337 - 366
8	X-RAY DIFFRACTION	8	A	367 - 398
9	X-RAY DIFFRACTION	9	A	399 - 417
10	X-RAY DIFFRACTION	10	A	418 - 468
11	X-RAY DIFFRACTION	11	A	469 - 497
12	X-RAY DIFFRACTION	12	A	498 - 537
13	X-RAY DIFFRACTION	13	A	538 - 583

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