PDB-4f5s: Crystal Structure of Bovine Serum Albumin

ID or keywords:

Entry

Database: PDB / ID: 4f5s

Title

Crystal Structure of Bovine Serum Albumin

Components

Serum albumin

Keywords

TRANSPORT PROTEIN / bovine serum albumin

Function / homology

Function and homology information

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

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.47 Å

Authors

Bujacz, A. / Bujacz, G.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of bovine, equine and leporine serum albumin.
Authors: Bujacz, A.

History

Deposition	May 13, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 3, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 27, 2018	Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4f5s.cif.gz	477.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4f5s.ent.gz	400.5 KB	Display	PDB format
PDBx/mmJSON format	4f5s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4f5s_validation.pdf.gz	456.2 KB	Display	wwPDB validaton report
Full document	4f5s_full_validation.pdf.gz	487.2 KB	Display
Data in XML	4f5s_validation.xml.gz	48 KB	Display
Data in CIF	4f5s_validation.cif.gz	67.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f5/4f5s ftp://data.pdbj.org/pub/pdb/validation_reports/f5/4f5s	HTTPS FTP

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Related structure data

Related structure data	4f5tC 4f5uC 4f5vC 1ao6S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3v09-d 4jk4-2 1hk1-d 4luf-d 4luh-d 2bxb-1 2bxb-2 5osw-d 4or0-1 2bxc-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (10) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (9) #37 - Jan 2003 Serum Albumin similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8)

Deposited unit

A: Serum albumin

B: Serum albumin

hetero molecules

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

1

A: Serum albumin

hetero molecules

defined by author&software
66.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Serum albumin

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

Unit cell

Length a, b, c (Å)	217.800, 44.989, 143.057
Angle α, β, γ (deg.)	90.00, 114.13, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Serum albumin / BSA Mass: 66561.969 Da / Num. of mol.: 2 / Fragment: Mature form of BSA, UNP residues 25-607 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02769
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% mmePEG 5000, 0.25M ammonium chloride, 0.1M MES 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2009 / Details: mirrors
Radiation	Monochromator: double crystal monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.47→40 Å / Num. obs: 43883 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / B_iso Wilson estimate: 66.4 Å² / R_merge(I) obs: 0.091 / Net I/σ(I): 11.4
Reflection shell	Resolution: 2.47→2.57 Å / Redundancy: 3 % / R_merge(I) obs: 0.549 / Mean I/σ(I) obs: 1.75 / Num. unique all: 3856 / % possible all: 84.9

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1AO6

1ao6

Resolution: 2.47→40 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.939 / SU B: 14.565 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.815 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25877	1369	3.1 %	RANDOM
R_work	0.1969	-	-	-
all	0.19898	43883	-	-
obs	0.19884	42357	94.61 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 72.554 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.58 Å²	0 Å²	-2.82 Å²
2-	-	-1.6 Å²	0 Å²
3-	-	-	-1.28 Å²

Refinement step

Cycle: LAST / Resolution: 2.47→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9306	0	10	327	9643

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	9576
X-RAY DIFFRACTION	r_angle_refined_deg	2.006	1.978	12956
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.082	5	1174
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.571	24.866	448
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.832	15	1767
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.254	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.131	0.2	1429
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	7163
X-RAY DIFFRACTION	r_mcbond_it	0.727	1.5	5869
X-RAY DIFFRACTION	r_mcangle_it	1.362	2	9504
X-RAY DIFFRACTION	r_scbond_it	2.402	3	3707
X-RAY DIFFRACTION	r_scangle_it	3.604	4.5	3447

LS refinement shell

Resolution: 2.471→2.535 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	78	-
R_work	0.27	2658	-
obs	-	-	81.48 %

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	0.3426	0.8133	0.7937	3.3702	1.0363	5.3166	-0.0688	0.1133	-0.1149	-0.6805	0.0782	-0.2178	-0.0304	0.3657	-0.0093	0.2651	-0.0041	-0.0265	0.1429	0.02	0.1533	9.2665	20.3761	81.6855
2	3.9897	1.6843	-1.5664	11.3249	-2.818	4.0184	0.0243	0.0529	0.1152	-0.1914	-0.0657	-1.3559	-0.1704	1.0282	0.0413	0.0489	-0.0802	0.0443	0.3649	-0.057	0.2029	22.5065	28.9378	95.9671
3	4.3816	3.1315	-0.2196	6.2739	-1.1486	0.9813	0.0691	-0.3321	0.5873	0.0485	-0.0716	-0.0502	-0.4378	0.3386	0.0025	0.2765	-0.1984	0.0663	0.2505	-0.0919	0.1528	16.0569	34.5816	102.6005
4	0.9957	-1.109	-1.1011	3.4473	0.8853	4.2361	0.0388	-0.038	-0.1263	-0.036	-0.0474	0.5979	-0.1521	-0.2514	0.0086	0.0575	-0.0188	-0.0556	0.133	0.0213	0.2381	-6.6445	24.6711	102.2385
5	3.3528	-1.0218	-3.1808	3.7793	2.3918	6.8888	0.1656	0.0464	0.6469	-0.2729	-0.0475	0.0796	-0.7582	0.1365	-0.118	0.251	0.0046	-0.0915	0.1146	0.0336	0.347	-3.5445	39.1107	100.1785
6	3.9583	2.7274	0.7768	5.5621	-1.3468	2.7929	0.1456	-0.2003	0.133	0.5994	-0.0493	0.4413	0.053	-0.7546	-0.0963	0.2164	0.0123	0.1496	0.4365	0.0082	0.3319	-21.0431	24.2316	114.9774
7	6.6638	4.9335	-2.0937	8.3106	-1.3772	3.6449	0.1953	-0.4322	-0.2392	1.0661	-0.1767	0.2393	0.2898	-0.3563	-0.0187	0.2602	0.0508	0.0201	0.3246	-0.0164	0.2677	-14.9112	16.4922	118.6317
8	42.0993	5.077	6.1421	0.6462	0.7873	0.9779	-0.058	-1.9423	0.9859	0.1057	-0.1876	0.2146	0.2043	-0.2944	0.2456	0.6893	0.0883	0.0953	0.5268	0.0642	0.4582	-2.0249	19.9527	128.3245
9	6.1732	-1.4276	-3.908	7.6163	5.0146	4.8134	-0.306	-1.335	0.1216	0.0007	0.0458	0.6353	0.1312	0.6273	0.2602	0.0442	0.1493	0.0292	0.5378	0.0777	0.1328	17.7373	12.6974	122.6999
10	5.4725	-1.5977	-1.0816	4.161	2.0514	3.4647	0.1406	-0.3221	0.2675	0.217	-0.0204	0.0458	-0.1311	-0.13	-0.1202	0.0592	-0.0066	0.0082	0.0437	0.0175	0.1002	11.1753	19.2459	116.1267
11	3.8518	-0.6158	-1.8187	2.9481	1.4077	1.3097	-0.2943	-0.7784	-0.7345	0.4221	-0.1484	0.4638	0.3184	0.2137	0.4427	0.1846	-0.0547	-0.0296	0.3441	0.2528	0.3753	6.113	5.7987	118.5337
12	5.6785	-0.0474	-0.9242	6.6087	0.5352	2.7581	-0.3521	-0.2549	0.1863	-0.4435	0.2823	-0.7532	0.2755	0.1545	0.0697	0.0891	0.0196	0.0451	0.0824	-0.0198	0.1262	30.7151	9.6356	117.8791
13	4.0684	-0.4803	-1.2417	5.874	1.1805	4.002	-0.1556	-0.4364	0.7516	0.3746	0.3436	-0.425	-0.2588	0.0194	-0.188	0.1336	0.1171	-0.1101	0.1945	-0.1011	0.2399	37.7657	10.9143	126.682
14	0.8155	1.0818	1.1633	3.0488	-1.1262	6.3003	-0.046	-0.1127	0.163	-0.1762	0.0825	0.3719	-0.1486	-0.4591	-0.0365	0.2573	-0.0195	-0.0279	0.1585	-0.0537	0.1848	47.4331	27.7289	70.2657
15	5.112	2.4416	-0.6464	8.2595	-0.44	2.817	0.097	-0.5134	-0.2487	0.5812	-0.1481	0.9212	0.2344	-0.5284	0.0511	0.1742	-0.0029	0.018	0.3627	-0.0094	0.1985	43.8587	19.2637	89.488
16	1.8752	2.0075	-0.3663	3.9976	-0.9873	2.8468	0.1934	-0.4179	-0.421	0.3655	-0.1381	0.1405	0.5033	-0.1361	-0.0553	0.2826	-0.0161	0.0277	0.307	0.1197	0.3196	52.6958	13.472	91.7239
17	1.2236	1.0745	0.3505	1.0766	0.0346	0.9096	-0.1609	-0.1282	-0.0116	-0.2507	-0.1248	-0.1874	0.1235	0.326	0.2857	0.2561	0.0432	0.0976	0.4273	-0.0641	0.2926	71.6333	23.3945	79.0243
18	8.7148	-1.1499	1.4708	2.5852	0.5289	1.6398	0.0619	-0.2758	-0.8847	0.4145	-0.0318	-0.123	0.8921	0.2072	-0.0301	0.5649	0.1294	0.0811	0.2719	0.0245	0.268	67.7529	9.0161	78.6553
19	4.6384	3.5171	-0.6231	4.2213	0.3367	1.7409	-0.1941	-0.2202	-0.1187	-0.422	0.2044	-0.6067	0.0457	0.4063	-0.0103	0.3645	0.0934	0.0393	0.4813	0.0069	0.3961	90.6454	23.2099	82.3752
20	3.8807	3.5371	-0.441	7.5487	-0.051	1.8935	-0.1318	-0.6106	0.3957	0.2225	-0.0384	-0.654	-0.2206	0.9969	0.1703	0.3	0.0219	-0.0301	0.7193	-0.033	0.407	87.1945	31.3768	88.5082
21	8.8781	-1.2206	-5.3124	0.1796	0.7255	3.2583	-0.3716	-0.6769	-0.6584	0.0537	0.0202	-0.0015	-0.004	0.5853	0.3514	0.7358	-0.0147	-0.0931	1.0057	-0.0121	0.7885	81.6212	27.857	103.6209
22	2.8056	2.2687	-0.9275	19.4626	-2.2344	2.8271	-0.0878	-0.4436	0.0758	0.393	0.1365	-0.3311	0.4328	0.6793	-0.0487	0.1718	0.177	-0.0013	0.281	-0.0141	0.0503	61.8415	35.559	109.5775
23	4.9477	-0.5805	-0.9004	3.5393	0.1956	3.6619	-0.1195	-0.0793	-0.5254	-0.0441	0.0371	-0.2656	0.2792	0.3884	0.0824	0.1546	0.0166	0.001	0.1756	-0.0113	0.1415	64.2324	28.6609	100.5357
24	3.0658	0.5104	-0.5467	2.4286	-0.3096	0.1633	-0.1503	-0.1976	0.5202	0.6604	0.0847	-1.0761	-0.1239	0.1861	0.0656	0.4972	-0.2789	-0.329	0.5596	-0.0907	0.6791	70.0376	42.134	99.9601
25	3.8191	3.5961	-1.6915	5.7808	-0.1001	2.5868	-0.1732	0.0631	0.1275	-0.0606	0.1413	0.2378	0.1174	-0.1464	0.032	0.118	0.0725	-0.0099	0.1455	-0.0351	0.1257	48.6499	38.595	112.5902
26	9.8212	1.1742	0.6839	3.8436	0.068	4.0501	-0.0318	-0.2558	-0.6289	0.2349	-0.0331	-0.1037	0.2671	0.3034	0.0649	0.0934	0.1048	-0.019	0.1489	-0.0026	0.0876	47.1777	36.7615	123.5898

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
14	X-RAY DIFFRACTION	14	B	1 - 106
15	X-RAY DIFFRACTION	15	B	107 - 147
16	X-RAY DIFFRACTION	16	B	148 - 198
17	X-RAY DIFFRACTION	17	B	199 - 250
18	X-RAY DIFFRACTION	18	B	251 - 295
19	X-RAY DIFFRACTION	19	B	296 - 336
20	X-RAY DIFFRACTION	20	B	337 - 366
21	X-RAY DIFFRACTION	21	B	367 - 398
22	X-RAY DIFFRACTION	22	B	399 - 417
23	X-RAY DIFFRACTION	23	B	418 - 468
24	X-RAY DIFFRACTION	24	B	469 - 497
25	X-RAY DIFFRACTION	25	B	498 - 537
26	X-RAY DIFFRACTION	26	B	538 - 583

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