PDB-5osw: Structure of caprine serum albumin in complex with 3,5-diiodosali...

ID or keywords:

Entry

Database: PDB / ID: 5osw

Title

Structure of caprine serum albumin in complex with 3,5-diiodosalicylic acid

Components

Albumin

Keywords

TRANSPORT PROTEIN / caprine serum albumin / goat serum albumin / 3 / 5-diiodosalicylic acid / DIU / orthorhombic crystal system

Function / homology

Function and homology information

enterobactin binding / blood microparticle / lipid binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Capra hircus (goat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Talaj, J.A. / Bujacz, A. / Bujacz, G.

Funding support

Poland, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structures of serum albumins from domesticated ruminants and their complexes with 3,5-diiodosalicylic acid.
Authors: Bujacz, A. / Talaj, J.A. / Zielinski, K. / Pietrzyk-Brzezinska, A.J. / Neumann, P.

History

Deposition	Aug 18, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 17, 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 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5osw.cif.gz	277.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5osw_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	5osw_full_validation.pdf.gz	2.9 MB	Display
Data in XML	5osw_validation.xml.gz	28.9 KB	Display
Data in CIF	5osw_validation.cif.gz	43.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/os/5osw ftp://data.pdbj.org/pub/pdb/validation_reports/os/5osw	HTTPS FTP

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Related structure data

Related structure data	5orfC 5oriSC 5otbC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4or0-1 4luh-d 6hn1-d 6m5e-1 6u4x-d 3lu7-1 4la0-1 2bxb-1 5orf-1 7mbl-d 2bxb-2 4g03-2 4luf-d 5iiu-d 6mdq-d 4f5s-2 6ocl-d 5otb-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 (9) #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)

Deposited unit

A: Albumin

hetero molecules

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

1

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

Unit cell

Length a, b, c (Å)	42.420, 66.060, 213.590
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	Albumin Mass: 66412.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / Plasmid details: serum plasma / Tissue: Blood / References: UniProt: B3VHM9

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Non-polymers , 5 types, 497 molecules

#2: Chemical	ChemComp-DIU / 2-HYDROXY-3,5-DIIODO-BENZOIC ACID / 2-HYDROXY-3,5-DIIODOBENZOIC ACID Mass: 389.914 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₇H₄I₂O₃
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Chemical	ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₀H₆₃NO₁₀
#5: Chemical	ChemComp-AE4 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₆
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.25 Å³/Da / Density % sol: 45.41 % / Description: rhomboid prism
Crystal grow	Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Jeffamine ED2001, Citric buffer pH 5, 0.01M BaCl2

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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: Sep 24, 2014 / Details: mirrors
Radiation	Monochromator: S 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.78→50 Å / Num. obs: 57982 / % possible obs: 98.7 % / Redundancy: 7.12 % / CC_1/2: 0.999 / R_merge(I) obs: 0.059 / Net I/σ(I): 20.16
Reflection shell	Resolution: 1.78→1.88 Å / Redundancy: 6.65 % / R_merge(I) obs: 0.951 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8312 / CC_1/2: 0.634 / % possible all: 95.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ORI

5ori

Resolution: 1.78→50.01 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.933 / SU B: 9.009 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24075	1188	2 %	RANDOM
R_work	0.17866	-	-	-
obs	0.17995	56794	98.74 %	-

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: 41.856 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.89 Å²	-0 Å²	0 Å²
2-	-	1.38 Å²	-0 Å²
3-	-	-	-0.49 Å²

Refinement step

Cycle: 1 / Resolution: 1.78→50.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4643	0	112	488	5243

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	4895
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.926	1.966	6621
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.094	5	588
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.077	25	222
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.478	15	880
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.165	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.136	0.2	714
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	3681
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	3.377	2.236	2337
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.916	3.336	2921
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.66	2.663	2558
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	5.015	21.276	8383
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	8.389	3	4895
X-RAY DIFFRACTION	r_sphericity_free	22.323	5	125
X-RAY DIFFRACTION	r_sphericity_bonded	11.695	5	5145

LS refinement shell

Resolution: 1.78→1.826 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	77	-
R_work	0.326	3860	-
obs	-	-	92.27 %

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	0.2576	0.1985	0.0032	0.7728	0.0415	0.0934	-0.0649	0.1468	0.1895	-0.0529	0.0311	0.1781	-0.0247	0.0098	0.0337	0.1997	0.0183	-0.0624	0.1337	0.0962	0.2558	3.2638	52.8533	70.3153
2	1.169	-0.6254	-0.2427	0.6492	0.1424	0.1031	-0.1475	0.0847	-0.0046	-0.2108	0.0861	0.1538	0.1024	0.0581	0.0615	0.4297	-0.0116	-0.0844	0.1449	0.1066	0.1004	9.7422	34.2231	63.6915
3	1.0417	0.2013	-0.2682	0.282	-0.2128	0.191	0.0199	0.0736	-0.0718	-0.1561	-0.066	0.0132	0.1002	0.0163	0.0461	0.2454	0.0568	0.0157	0.1786	0.0156	0.1975	16.2569	30.5864	71.4409
4	0.0402	0.0859	-0.0546	0.2221	-0.1389	0.5444	0.0093	-0.026	0.0495	0.0088	-0.0754	0.0285	0.0058	0.0103	0.0661	0.1698	0.0127	-0.0222	0.1554	0.0098	0.2446	8.799	41.1142	92.9262
5	0.7647	-0.486	0.5997	0.8949	-0.2484	0.5173	0.013	-0.0216	0.0435	-0.0488	0.0133	-0.053	-0.0037	0.0085	-0.0263	0.1675	0.0094	-0.0136	0.1438	0.0116	0.2489	22.5637	40.8009	88.0912
6	0.8485	-0.0061	-0.5484	0.0111	-0.1215	1.7956	-0.0996	-0.0375	0.0991	0.0221	-0.0045	-0.0128	-0.1374	0.1228	0.1041	0.2028	0.039	-0.0516	0.1696	0.0159	0.1965	10.3852	35.6615	111.9358
7	0.667	0.0298	-1.1021	0.2998	0.1561	3.0207	-0.1548	0.0223	0.0944	-0.0318	0.0582	0.0149	0.0206	-0.1481	0.0966	0.1569	0.066	-0.0203	0.2004	-0.011	0.1724	2.147	29.9566	109.8195
8	0.2224	-0.1004	0.0646	1.6102	2.2825	3.4491	-0.0547	-0.1078	-0.1045	0.0549	0.0587	0.0662	0.0843	0.0029	-0.004	0.214	0.0242	0.0203	0.169	0.0303	0.1732	4.4056	15.9421	102.0717
9	1.496	0.152	0.1721	0.444	0.2282	0.1284	0.0346	-0.0172	0.1157	-0.005	-0.0245	-0.0492	0.0311	-0.0164	-0.0101	0.2055	0.0149	0.0155	0.1873	0.0053	0.1858	-5.7666	12.7294	82.8838
10	1.149	-0.014	0.0924	0.1709	0.0513	0.0259	-0.0414	-0.0202	0.0278	-0.0311	0.0225	-0.0161	-0.004	0.0077	0.0188	0.1934	0.0229	-0.0046	0.1695	0.0172	0.1958	1.408	21.5169	84.4796
11	0.0902	-0.142	-0.1721	0.3963	0.5184	0.6895	0.0268	-0.0237	0.0445	0.0356	-0.0917	0.0088	0.0503	-0.1256	0.0649	0.1573	-0.014	-0.0093	0.1962	0.008	0.2327	-10.8968	22.3257	91.6511
12	0.8915	-0.1557	-1.7451	0.4085	0.5601	3.7291	-0.1182	0.1506	-0.0088	-0.1842	-0.0459	0.2801	0.1138	-0.1493	0.164	0.3335	0.0346	-0.0602	0.1918	-0.0399	0.2551	-10.8861	9.2043	70.4516
13	1.0273	0.9389	-0.9235	1.0424	-0.1969	3.1344	-0.0751	0.0493	-0.1217	-0.028	-0.025	-0.1196	0.2824	-0.2133	0.1001	0.2543	0.131	0.0404	0.2288	0.0251	0.0782	-11.0785	-0.8825	68.8155

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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