PDB-5ori: Structure of caprine serum albumin in orthorhombic crystal system

ID or keywords:

Entry

Database: PDB / ID: 5ori

Title

Structure of caprine serum albumin in orthorhombic crystal system

Components

Albumin

Keywords

TRANSPORT PROTEIN / caprine serum albumin / goat serum albumin /

orthorhombic crystal system

Function / homology

Function and homology information

lipid binding /

extracellular space /

metal ion binding
Similarity search - Function

Biological species

Capra hircus (goat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.94 Å

Authors

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

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 16, 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ori.cif.gz	252.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ori.ent.gz	205.6 KB	Display	PDB format
PDBx/mmJSON format	5ori.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	5orfC 5oswC 5otbC 4lufS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4g03-1 3lu8-1 1ao6-1 6fak-d 5otb-1 3lu6-2 4la0-2 5osw-d 2vue-1 5iiu-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)

Deposited unit

A: Albumin

66.4 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)	42.270, 66.960, 213.290
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.27 Å³/Da / Density % sol: 46 % / Description: rhomboid prism
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Jeffamine ED2001, citric buffer pH 5.0, 0.02M BaCl2

-
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 23, 2014 / Details: mirrors
Radiation	Monochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.94→50 Å / Num. obs: 45413 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Redundancy: 5.17 % / B_iso Wilson estimate: 50 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.056 / Net I/σ(I): 18.77
Reflection shell	Resolution: 1.94→2.04 Å / Redundancy: 4.38 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 5899 / CC_1/2: 0.626 / % possible all: 93.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LUF

4luf

Resolution: 1.94→39.3 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.924 / SU B: 8.961 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.167 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2483	2272	5 %	RANDOM
R_work	0.18846	-	-	-
obs	0.19143	43138	98.73 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 50.088 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.53 Å²	-0 Å²	0 Å²
2-	-	0.1 Å²	-0 Å²
3-	-	-	1.43 Å²

Refinement step

Cycle: 1 / Resolution: 1.94→39.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4643	0	0	293	4936

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.019	4792
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.035	1.977	6490
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.786	5	592
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.233	25.044	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.671	15	881
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.701	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.148	0.2	713
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	3601
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	5.38	4.056	2341
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.894	6.059	2927
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.57	4.272	2451
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	6.835		7835
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	9.341	3	4792
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded	24.515	5	4673

LS refinement shell

Resolution: 1.94→1.99 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.383	155	-
R_work	0.317	2922	-
obs	-	-	92.35 %

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	0.0287	0.0837	-0.0731	0.4752	-0.1235	0.2756	-0.0207	0.012	0.0257	-0.1418	0.0078	0.1542	-0.0159	-0.0036	0.0129	0.1286	0.0166	-0.0611	0.068	0.0096	0.1338	2.6048	53.0398	70.7981
2	0.3731	-0.0867	0.0526	0.3054	0.151	0.1053	0.0073	0.0393	0.0082	-0.1919	-0.0317	0.1082	-0.0833	0.0333	0.0244	0.2132	0.005	-0.0401	0.1046	-0.0079	0.0554	9.2058	34.8875	64.2014
3	0.7905	0.0573	-0.3729	0.3658	0.2683	0.4275	-0.0415	0.0461	-0.015	-0.1012	0.0123	0.0569	-0.0385	-0.0073	0.0293	0.1412	0.0073	-0.0171	0.0819	-0.0048	0.0832	16.0288	31.148	71.4721
4	0.0229	0.0628	0.0022	0.1789	0.0094	0.0065	-0.0033	-0.017	0.0153	-0.0129	-0.0207	0.0487	-0.0069	0.0178	0.024	0.087	0.0086	-0.0059	0.107	0.0042	0.108	8.7453	41.6041	93.3717
5	0.2567	-0.1037	0.1642	0.1844	-0.0552	0.2254	-0.0008	0.002	-0.008	-0.0207	0.0029	-0.0231	-0.0195	0.0065	-0.0021	0.0912	0.0012	-0.0031	0.09	0.0006	0.0999	22.4216	41.0937	88.2783
6	0.7188	-0.1201	-0.3426	0.1642	-0.1044	0.3487	0.0083	-0.0007	0.0215	0.0539	-0.0148	-0.0143	-0.0575	0.0403	0.0064	0.1006	-0.0002	-0.0063	0.0991	0.0025	0.083	10.0364	36.1509	111.9463
7	0.1376	0.0764	-0.1903	0.0851	-0.205	0.5099	0.0218	0.0238	-0.021	0.0103	0.0243	0.0264	-0.0187	-0.0193	-0.0461	0.0952	0.0087	-0.0006	0.0919	-0.0061	0.0909	1.838	30.4949	109.6019
8	0.0076	-0.0051	-0.002	0.5956	0.9094	1.399	0.0243	-0.0134	-0.0069	0.0244	-0.0055	-0.0074	0.0394	-0.0433	-0.0188	0.1023	0.0074	0.003	0.0899	0.0096	0.091	4.2344	15.8706	101.8436
9	0.3156	0.0567	-0.065	0.1335	0.1051	0.1243	-0.0419	0.0121	0.0139	0.0144	0.0242	0.0304	0.0328	0.0233	0.0176	0.0988	0.0049	0.0008	0.0944	0.0001	0.0916	-5.8299	12.9006	82.9872
10	0.5175	-0.2233	0.1607	0.107	-0.0672	0.194	0.0185	0.0007	0.0937	-0.0342	-0.0074	-0.0351	0.0325	0.022	-0.0111	0.0828	0.0012	0.0054	0.0935	-0.0034	0.1055	1.4773	21.549	84.8867
11	0.1217	0.1023	0.1382	0.2406	0.2106	0.2198	-0.0182	-0.0111	0.0272	0.0083	0.0147	-0.0136	0.0058	-0.0161	0.0034	0.0893	-0.0048	-0.0031	0.0972	-0.0005	0.1096	-11.0634	22.4875	91.7839
12	0.0141	-0.0057	0.0239	0.3636	0.3024	0.3111	0.0065	0.0162	-0.0212	-0.0767	-0.0089	0.0812	-0.0013	0.0578	0.0024	0.1457	0.0261	-0.0126	0.1041	-0.0044	0.091	-10.3705	10.1773	70.3385
13	0.5289	0.3582	-0.4511	0.2748	-0.2067	0.7151	-0.0603	0.0404	-0.0245	0.0114	0.0131	-0.0151	0.2538	-0.0403	0.0472	0.1597	0.0414	-0.0033	0.1109	0.0027	0.0648	-10.8575	-0.2807	68.6025

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

-
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

-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

-
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