PDB-4f5u: Crystal structure of Equine Serum Albumin at 2.04 resolution

ID or keywords:

Entry

Database: PDB / ID: 4f5u

Title

Crystal structure of Equine Serum Albumin at 2.04 resolution

Components

Serum albumin

Keywords

TRANSPORT PROTEIN / Equine serum albumin / helical protein

Function / homology

Function and homology information

enterobactin binding / cellular response to calcium ion starvation / 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: 2.04 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	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 / diffrn_source / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4f5u.cif.gz	251.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4f5u.ent.gz	204.3 KB	Display	PDB format
PDBx/mmJSON format	4f5u.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4f5u_validation.pdf.gz	478.9 KB	Display	wwPDB validaton report
Full document	4f5u_full_validation.pdf.gz	516.3 KB	Display
Data in XML	4f5u_validation.xml.gz	31.7 KB	Display
Data in CIF	4f5u_validation.cif.gz	45.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f5/4f5u ftp://data.pdbj.org/pub/pdb/validation_reports/f5/4f5u	HTTPS FTP

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Related structure data

Related structure data	4f5sC 4f5tSC 4f5vC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6a7p-2 2xvu-1 4s1y-d 4j2v-d 4emx-2 3v03-1 2vuf-1 4ot2-d 2px0-2 5x52-2 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 (9) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Serum albumin

hetero molecules

66.7 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)	89.254, 89.254, 134.802
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: 65854.203 Da / Num. of mol.: 1 / Fragment: UNP residues 25-607 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747
#2: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₄
#4: Chemical	ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₅
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.35 Å³/Da / Density % sol: 47.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 80% Tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.932 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2011 / Details: mirrors
Radiation	Monochromator: Double crystal monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.932 Å / Relative weight: 1
Reflection	Resolution: 2.04→50 Å / Num. obs: 38668 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / R_merge(I) obs: 0.11 / Net I/σ(I): 16.7
Reflection shell	Resolution: 2.04→2.11 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.639 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4F5T

4f5t

Resolution: 2.04→50 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.936 / SU B: 11.617 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24294	1211	3.1 %	RANDOM
R_work	0.19612	-	-	-
obs	0.19756	37399	99.84 %	-
all	-	38668	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 41.582 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.99 Å²	0.99 Å²	0 Å²
2-	-	1.99 Å²	0 Å²
3-	-	-	-2.98 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4609	0	59	345	5013

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	4833
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.966	1.991	6538
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.225	5	599
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.897	25	222
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.735	15	879
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.427	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	711
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	3664
X-RAY DIFFRACTION	r_gen_planes_other
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	0.825	1.5	2954
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.445	2	4767
X-RAY DIFFRACTION	r_scbond_it	2.557	3	1879
X-RAY DIFFRACTION	r_scangle_it	3.946	4.5	1762
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.04→2.093 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.366	87	-
R_work	0.33	2732	-
obs	-	-	98.84 %

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	1.7128	0.4847	0.0558	2.8261	0.7532	1.2141	0.1136	0.1162	0.081	0.1231	0.023	0.2861	0.0048	-0.2314	-0.1365	0.1882	0.0868	-0.0288	0.1181	0.0112	0.1958	-15.0501	53.9179	68.1691
2	1.9471	0.0291	-0.649	4.9162	-0.4839	0.5932	0.1185	0.3562	0.2362	-0.6181	-0.1101	-0.1338	-0.1107	-0.0467	-0.0084	0.3284	0.117	-0.0348	0.2082	0.001	0.1821	0.114	54.2591	54.8582
3	1.2332	0.2424	-0.0364	4.2911	-1.7726	0.9861	0.1829	0.2597	0.1303	-0.2551	-0.2971	-0.4159	-0.1858	0.2576	0.1143	0.4742	-0.01	0.0725	0.2358	0.0131	0.2599	8.5286	53.9867	60.8865
4	1.5765	-1.2426	-0.0989	3.1783	1.2593	2.2516	-0.108	-0.0887	-0.032	0.1908	-0.0162	0.3525	-0.0443	-0.0288	0.1242	0.0756	0.0101	0.0115	0.0439	-0.0379	0.0729	3.3589	42.4483	80.4591
5	3.5863	-1.7671	0.3588	3.1675	0.0656	3.0128	0.1066	-0.0764	0.2755	-0.0815	-0.0372	-0.2432	-0.47	0.184	-0.0694	0.2105	-0.0474	0.0181	0.0436	-0.059	0.1365	9.4661	54.915	80.3783
6	1.4341	1.4987	0.4872	7.9697	-0.5669	2.7238	-0.0423	-0.2488	-0.1795	0.7194	-0.0489	0.0481	0.0834	0.0718	0.0911	0.1969	0.0649	0.0304	0.2384	-0.0258	0.1438	13.3956	32.4829	92.9386
7	2.6709	1.3491	0.0306	2.13	-2.2052	7.2534	0.083	-0.2131	-0.3032	0.1096	0.0243	0.1636	0.5016	-0.3162	-0.1073	0.1658	0.046	0.0428	0.1244	-0.0134	0.1868	12.226	25.5794	85.6224
8	2.3121	2.7094	-5.2683	3.6303	-8.7229	26.4313	-0.2011	-0.1182	-0.3995	-0.1782	-0.2499	-0.3729	0.2845	0.774	0.451	0.195	0.1472	0.0691	0.2231	0.0336	0.3422	21.1338	26.365	74.2207
9	6.4997	0.6246	-0.859	1.8114	0.5339	2.118	-0.1158	0.0825	0.0046	-0.0641	0.0816	-0.005	0.0867	0.2842	0.0343	0.0515	0.0491	0.0053	0.0982	-0.0138	0.0285	13.1252	28.2978	54.6325
10	2.0914	0.2555	1.3715	1.1062	1.1577	3.5255	0.0247	0.0493	0.0349	-0.0411	-0.0153	-0.0679	-0.1315	0.2329	-0.0094	0.0635	0.0104	0.0091	0.054	-0.0226	0.0785	10.5684	35.2334	62.3075
11	2.6603	1.1551	0.4483	5.802	1.5988	5.13	-0.1421	-0.0065	-0.2239	0.2419	0.1113	0.1682	0.7509	0.0592	0.0307	0.1433	0.0398	0.0389	0.0757	-0.0069	0.1068	5.2114	22.3397	64.3905
12	2.7969	1.1241	-0.1531	3.3264	-2.6126	4.8181	-0.0023	0.3455	0.0666	0.1578	0.0237	0.0884	0.0219	-0.0809	-0.0214	0.0789	0.0661	0.0133	0.1932	-0.0287	0.0936	9.4248	30.5077	42.2878
13	1.5977	0.0287	0.8246	2.8404	-1.4545	3.3265	0.0628	0.3896	0.0721	-0.0502	-0.0841	-0.0285	0.0798	0.4018	0.0213	0.0402	0.0783	0.0232	0.262	-0.0205	0.1034	17.1041	28.3707	36.691

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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