PDB-4luf: Crystal Structure of Ovine Serum Albumin

ID or keywords:

Entry

Database: PDB / ID: 4luf

Title

Crystal Structure of Ovine Serum Albumin

Components

Serum albumin

Keywords

TRANSPORT PROTEIN / Helical structure / transport /

Fatty acids /

metabolites

Function / homology

Function and homology information

enterobactin binding /

lipid binding /

extracellular space /

metal ion binding
Similarity search - Function

Biological species

Ovis aries (sheep)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

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

Citation

Journal: To be Published
Title: Crystal structure of ovine serum albumin and its complex with 3,5-diiodosalicylic acid
Authors: Bujacz, A. / Talaj, J.A. / Pietrzyk, A.J.

History

Deposition	Jul 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4luf.cif.gz	248.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4luf.ent.gz	202 KB	Display	PDB format
PDBx/mmJSON format	4luf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lu/4luf ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4luf	HTTPS FTP

-
Related structure data

Related structure data	4luhC 4f5sS 1ao6 4f5u 4f5v S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6u4x-d 4jk4-2 3lu6-1 2xw1-2 5otb-2 4f5s-1 7mbl-d 6u5a-d 4f5t-d 5osw-d 6m5e-1 5otb-3 5yxe-d 1uor-d 5otb-4 6oci-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#37 - Jan 2003 Serum Albumin similarity (9) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone 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

68 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)	118.390, 118.390, 120.820
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-836- HOH
2	1	A-879- HOH

-
Protein , 1 types, 1 molecules A

#1: Protein	Serum albumin / Mass: 66427.820 Da / Num. of mol.: 1 / Fragment: Mature form of ovine serum albumin / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P14639

-
Non-polymers , 7 types, 202 molecules

#2: Chemical	ChemComp-2Q5 / (2R)-2-{[(2R)-2-{[(2S)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propyl]oxy}propan-1-ol Mass: 250.332 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₅
#3: Chemical	ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₅
#4: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-MLI / MALONATE ION / Malonic acid Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#6: Chemical	ChemComp-SIN / SUCCINIC ACID / Succinic acid Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₄
#7: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.68 Å³/Da / Density % sol: 66.57 %
Crystal grow	Temperature: 293 K / pH: 7 Details: Tacsimate 70%, 4% PPG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2013 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 43652 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.69 % / B_iso Wilson estimate: 46.1 Å² / R_merge(I) obs: 0.096 / Net I/σ(I): 12.11
Reflection shell	Resolution: 2.3→2.4 Å / Redundancy: 3.73 % / R_merge(I) obs: 0.902 / Mean I/σ(I) obs: 2 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
MOSFLM		data reduction
PHASER		phasing
REFMAC	5.7.0032	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F5S

4f5s

Resolution: 2.3→47.19 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.927 / SU B: 10.471 / SU ML: 0.119 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	1311	3 %	RANDOM
R_work	0.176	-	-	-
obs	0.177	42338	99.4 %	-
all	-	43914	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 47.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.66 Å²	0.66 Å²	0 Å²
2-	-	0.66 Å²	0 Å²
3-	-	-	-2.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→47.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4645	0	105	191	4941

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	4873
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.138	1.993	6578
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.815	5	588
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.642	25.022	225
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.573	15	876
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.901	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.132	0.2	723
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	3642
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	3.203	3.42	2338
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	4.592	5.116	2921
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.078	4.085	2535
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	10.353	29.854	7722
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	97	-
R_work	0.273	3099	-
obs	-	-	99.69 %

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	0.4108	0.2664	-0.3823	0.9798	-0.1737	0.419	0.0752	0.0954	-0.0073	-0.1541	-0.0417	-0.101	-0.0382	-0.1335	-0.0335	0.1158	0.0052	0.0116	0.0832	0.0194	0.0611	63.3258	-17.6146	-6.7732
2	0.1174	-0.1338	0.0894	0.3645	0.1978	0.5047	-0.03	0.013	-0.0027	0.1892	0.0363	0.022	0.2008	0.0689	-0.0064	0.1275	0.0151	0.0033	0.059	-0.0097	0.1251	67.4671	-35.1821	4.1878
3	1.0933	-0.7381	-0.2077	1.2449	0.1613	0.0971	-0.0728	-0.3303	0.2114	0.0932	0.1029	0.0137	0.1303	0.0879	-0.0301	0.2456	0.0699	0.0264	0.1305	-0.0804	0.077	68.5729	-31.8576	14.1917
4	0.1545	-0.1138	-0.3356	0.4382	0.4464	0.8504	0.0125	0.0513	0.0552	0.0409	0.0824	-0.0377	0.0369	-0.0498	-0.0949	0.1154	0.0004	0.0243	0.0581	0.0234	0.1049	54.6247	-11.2864	16.8782
5	1.3043	0.1506	-0.7268	0.5199	0.7561	1.8546	-0.0515	-0.0467	0.1698	0.0756	0.1511	-0.0111	0.1748	0.3115	-0.0996	0.1002	0.0261	-0.0054	0.0619	-0.0045	0.103	68.7056	-12.3727	20.9261
6	2.5779	-0.1267	0.4514	0.0106	-0.0566	0.4713	0.0172	-0.0512	0.1374	0.0001	-0.0007	-0.0123	-0.0688	-0.0207	-0.0165	0.1525	0.047	0.0076	0.0245	0.0186	0.0858	45.8352	-2.8565	33.8534
7	1.9161	-1.921	0.4597	2.0381	-0.1862	0.8465	-0.0477	-0.0992	-0.1175	0.0802	0.0335	0.103	0.0646	-0.2203	0.0142	0.0696	-0.0103	-0.0043	0.0891	0.0044	0.109	38.4068	-9.6524	31.6844
8	1.1271	-2.7151	-0.2178	8.4292	1.6394	0.7037	-0.1013	-0.1568	-0.1188	0.3935	0.1661	0.1908	0.126	-0.0866	-0.0648	0.1164	-0.0086	0.0521	0.0555	0.0373	0.0933	40.9697	-24.9362	35.7853
9	1.2428	-0.7643	0.8492	2.1283	0.0652	0.7986	-0.0187	-0.0821	-0.0299	0.1376	-0.0105	0.0447	0.0308	-0.105	0.0291	0.0844	-0.076	-0.0122	0.0945	-0.0228	0.0988	40.5832	-40.8533	21.0188
10	0.966	0.437	0.9299	0.4082	0.7681	1.538	0.0256	0.0979	-0.042	0.0311	0.0837	-0.0614	0.0196	0.0763	-0.1092	0.1029	-0.0197	-0.0146	0.1155	0.0037	0.0605	47.959	-31.9152	20.1335
11	0.6604	0.1723	0.3145	1.0634	0.4128	0.5966	0.07	0.0109	0.1933	0.0744	-0.2221	0.2659	-0.0005	0.0134	0.1522	0.0583	-0.0512	0.0103	0.0936	-0.0336	0.1177	34.1709	-28.7163	17.7761
12	0.0181	0.0387	0.0534	0.8921	0.8138	0.7635	0.072	0.0116	0.0297	0.2492	-0.0254	-0.1324	0.2619	-0.0472	-0.0466	0.1324	-0.0063	0.0268	0.1044	0.0081	0.1123	42.3417	-51.7596	12.8023
13	1.998	-1.4475	-1.0304	1.1528	1.1272	2.4504	-0.1598	-0.179	-0.1065	0.2817	0.1209	0.072	0.5378	0.1443	0.0389	0.2922	-0.0476	-0.0034	0.0529	0.0171	0.0168	40.929	-61.4525	16.7066

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

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 7 types, 202 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 1 molecules A

-Non-polymers , 7 types, 202 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 7 types, 202 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi