PDB-7fyw: Crystal Structure of apo mouse FABP5, twinned in P21 with beta=90deg

ID or keywords:

Entry

Database: PDB / ID: 7fyw

Title

Crystal Structure of apo mouse FABP5, twinned in P21 with beta=90deg

Components

Fatty acid-binding protein 5

Keywords

LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING

Function / homology

Function and homology information

Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / lipid transport across blood-brain barrier / retrograde trans-synaptic signaling by endocannabinoid / negative regulation of D-glucose transmembrane transport / positive regulation of peroxisome proliferator activated receptor signaling pathway / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.81 Å

Authors

Ehler, A. / Benz, J. / Obst, U. / Rudolph, M.G.

Funding support

Switzerland, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2025
Title: A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands.
Authors: Ehler, A. / Bartelmus, C. / Benz, J. / Plitzko, I. / Rudolph, M.G.

History

Deposition	Apr 27, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 14, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Aug 13, 2025	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7fyw.cif.gz	229.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7fyw.ent.gz	186.4 KB	Display	PDB format
PDBx/mmJSON format	7fyw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7fyw_validation.pdf.gz	459.8 KB	Display	wwPDB validaton report
Full document	7fyw_full_validation.pdf.gz	475.4 KB	Display
Data in XML	7fyw_validation.xml.gz	24.1 KB	Display
Data in CIF	7fyw_validation.cif.gz	32.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/7fyw ftp://data.pdbj.org/pub/pdb/validation_reports/fy/7fyw	HTTPS FTP

-
Group deposition

ID	G_1002264 (222 entries) 7fvu 7fvv 7fvw 7fvx 7fvy 7fvz 7fw0 7fw1 7fw2 7fw3
Title	To be published
Type	undefined
Description	A set of fabp crystal structures

-
Related structure data

Similar structure data	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	#155 - Nov 2012 Vitamin D Receptor similarity (1) #193 - Jan 2016 Siderocalin similarity (3) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #88 - Apr 2007 Clathrin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #166 - Oct 2013 Proteasome similarity (1) #176 - Aug 2014 Dynein similarity (1) #177 - Sep 2014 Apoptosomes similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #78 - Jun 2006 Luciferase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#193 - Jan 2016
Siderocalin
similarity (3)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#88 - Apr 2007
Clathrin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#166 - Oct 2013
Proteasome
similarity (1)
#176 - Aug 2014
Dynein
similarity (1)
#177 - Sep 2014
Apoptosomes
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#78 - Jun 2006
Luciferase
similarity (1)

Deposited unit

A: Fatty acid-binding protein 5

B: Fatty acid-binding protein 5

C: Fatty acid-binding protein 5

D: Fatty acid-binding protein 5

hetero molecules

61.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fatty acid-binding protein 5

hetero molecules

defined by author&software
Evidence: gel filtration, elutes as a monomer
15.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fatty acid-binding protein 5

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

3

C: Fatty acid-binding protein 5

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

4

D: Fatty acid-binding protein 5

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

Unit cell

Length a, b, c (Å)	59.625, 75.128, 61.805
Angle α, β, γ (deg.)	90.000, 90.180, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fatty acid-binding protein 5 / Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / ...Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / Keratinocyte lipid-binding protein / Psoriasis-associated fatty acid-binding protein homolog / PA-FABP Mass: 15440.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp5, Fabpe, Klbp, Mal1 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05816
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Operator: h,-k,-l / Fraction: 0.473

Reflection

Resolution: 1.83→42.98 Å / Num. obs: 25292 / % possible obs: 99.2 % / Redundancy: 6.36 % / CC_1/2: 0.998 / R_merge(I) obs: 0.083 / R_rim(I) all: 0.09 / R_sym value: 0.083 / Χ²: 0.872 / Net I/σ(I): 10.02 / Num. measured all: 167736 / Scaling rejects: 26

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.81-1.86	6.259	1.449	1.29	11792	1896	1884	0.689	1.581	99.4
1.86-1.91	6.398	1.025	1.87	11893	1875	1859	0.75	1.116	99.1
1.91-1.96	6.621	0.788	2.64	12011	1826	1814	0.852	0.856	99.3
1.96-2.02	6.794	0.508	3.77	11835	1750	1742	0.94	0.551	99.5
2.02-2.09	6.6	0.412	4.63	11319	1726	1715	0.952	0.448	99.4
2.09-2.16	6.539	0.315	5.78	10744	1654	1643	0.969	0.343	99.3
2.16-2.25	6.261	0.256	6.86	10049	1612	1605	0.976	0.279	99.6
2.25-2.34	6.39	0.201	8.61	9751	1533	1526	0.987	0.22	99.5
2.34-2.44	6.741	0.16	10.54	10031	1491	1488	0.992	0.174	99.8
2.44-2.56	6.687	0.133	12.47	9382	1407	1403	0.993	0.145	99.7
2.56-2.7	6.492	0.112	14.12	8913	1376	1373	0.995	0.122	99.8
2.7-2.86	6.139	0.099	16.03	7926	1293	1291	0.993	0.109	99.8
2.86-3.06	6.273	0.083	18.98	7490	1198	1194	0.996	0.09	99.7
3.06-3.3	6.542	0.071	21.88	7478	1145	1143	0.997	0.077	99.8
3.3-3.62	6.33	0.062	24.28	6659	1053	1052	0.997	0.067	99.9
3.62-4.05	5.909	0.059	24.3	5702	966	965	0.997	0.065	99.9
4.05-4.67	5.791	0.054	25.26	4876	847	842	0.997	0.059	99.4
4.67-5.72	6.267	0.049	26.25	4631	742	739	0.998	0.054	99.6
5.72-8.09	5.692	0.052	24.57	3307	583	581	0.996	0.057	99.7
8.09-42.977	5.563	0.04	24.87	1947	356	350	0.998	0.045	98.3

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	dev_728	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.81→42.977 Å / FOM work R set: 0.7319 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.02 / Stereochemistry target values: TWIN_LSQ_F
Details: beautiful example of almost perfectly merohedrally twinned monoclinic form with beta=90deg, emulating orthorhombic symmetry. molecular replacement in 2mmm clashes for all space groups. ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2514	2506	5.17 %	RANDOM
R_work	0.2059	45997	-	-
obs	0.208	48458	97.37 %	-

Solvent computation

Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.29 Å² / k_sol: 0.33 e/Å³

Displacement parameters

B_iso max: 158.28 Å² / B_iso mean: 46.76 Å² / B_iso min: 17.27 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.4695 Å²	0 Å²	0.3241 Å²
2-	-	7.3693 Å²	-0 Å²
3-	-	-	-0.8998 Å²

Refinement step

Cycle: final / Resolution: 1.81→42.977 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4244	0	1	127	4372
B_iso mean	-	-	41.4	31.75	-
Num. residues	-	-	-	-	548

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	4298
X-RAY DIFFRACTION	f_angle_d	0.952	5761
X-RAY DIFFRACTION	f_chiral_restr	0.061	660
X-RAY DIFFRACTION	f_plane_restr	0.003	728
X-RAY DIFFRACTION	f_dihedral_angle_d	15.729	1616

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 17

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8101-1.847	0.3787	147	0.3963	2624	2771	91
1.847-1.8872	0.3649	152	0.3895	2637	2789	90
1.8872-1.9311	0.4496	129	0.3983	2669	2798	90
1.9311-1.9794	0.3306	130	0.3228	2651	2781	92
1.9794-2.0329	0.3778	141	0.3157	2704	2845	92
2.0329-2.0927	0.3232	129	0.318	2610	2739	91
2.0927-2.1602	0.2969	134	0.2932	2728	2862	93
2.1602-2.2374	0.321	153	0.2961	2717	2870	93
2.2374-2.327	0.32	142	0.2885	2649	2791	91
2.327-2.4329	0.3173	135	0.2718	2739	2874	94
2.4329-2.5611	0.3443	164	0.256	2709	2873	92
2.5611-2.7216	0.2539	130	0.2546	2717	2847	93
2.7216-2.9316	0.2807	154	0.2287	2743	2897	93
2.9316-3.2265	0.2566	149	0.1996	2736	2885	94
3.2265-3.693	0.2132	155	0.1493	2763	2918	93
3.693-4.6515	0.181	151	0.1144	2769	2920	94
4.6515-37.5721	0.2184	154	0.1545	2832	2986	94

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	3.0809	0.3755	0.3765	2.4308	0.0477	2.3536	-0.2644	0.5054	-0.1821	0.1474	0.0777	-0.1105	-0.1133	0.0583	0.1791	0.0717	-0.0013	0.0089	0.3407	0.0116	0.2091	17.6505	-1.3099	21.6792
2	1.7286	-0.5233	2.0298	0.8421	-0.471	3.7508	-0.1571	-0.1847	0.0292	0.2122	-0.1068	-0.1611	-0.1159	0.0269	-0.6364	0.1415	-0.1311	-0.0413	0.7899	0.0996	0.172	27.3069	-3.2514	20.8437
3	1.0855	0.8573	-1.1527	6.1935	0.95	1.851	0.3477	-0.7456	-0.4416	-0.2957	0.0231	0.0076	0.1247	-0.7176	-0.2329	0.173	-0.087	-0.0023	0.6531	-0.0784	0.2324	21.2441	0.142	8.5618
4	3.8452	1.5268	2.3237	0.9092	0.813	1.4452	-0.1229	-0.3075	-0.0426	0.0521	-0.3247	0.2113	0.0648	-0.106	0.1269	0.1913	-0.1256	-0.0083	0.7676	-0.0409	0.2865	27.1495	-3.6672	11.389
5	3.8108	-2.3925	2.7259	3.4039	-1.933	3.7397	0.1078	1.3306	-0.484	-0.0452	-0.283	0.0732	0.4722	0.1421	0.1772	0.2494	-0.0139	-0.0284	0.5431	-0.0764	0.3448	17.863	-10.6371	9.5313
6	4.1567	-0.4078	0.3728	5.6248	-1.2245	3.807	-0.0539	0.286	-0.6671	0.1841	0.2243	-0.2724	0.4314	-0.5446	-0.1165	0.1703	-0.0294	-0.0334	0.3525	-0.1013	0.2726	13.5608	-8.8996	16.6127
7	2.9576	2.0407	-1.3732	7.3249	-2.0141	2.9775	0.2279	0.2577	-0.102	0.8391	-0.0021	0.1521	-0.0368	0.0056	-0.2036	0.3307	0.0222	-0.0542	0.3696	-0.0623	0.2117	16.2695	-1.7444	23.8798
8	3.0595	0.2758	-0.3691	1.5169	-0.1825	5.5312	0.2243	-0.5721	-0.5564	0.4024	0.008	-0.2363	0.2582	-0.3939	-0.2023	0.2295	-0.016	-0.0856	0.3558	0.0673	0.3042	27.311	-5.7741	49.8536
9	6.8469	1.6396	-2.5106	1.5012	-1.5281	2.2079	0.1864	-0.5207	0.871	0.386	0.1546	0.2259	-0.3166	-0.6917	-0.1662	0.2878	0.1751	0.0029	0.8632	-0.1774	0.3295	15.2382	12.3048	57.7317
10	4.4757	-1.0226	-1.0841	3.0132	-0.0031	1.1214	-0.1835	-0.5209	0.098	0.107	0.1819	0.0955	-0.0582	0.6215	-0.0061	0.1586	-0.0212	-0.0334	0.4727	-0.0154	0.1836	17.6675	0.2807	42.5494
11	3.0455	0.2062	-0.0555	3.4574	0.9477	2.8984	-0.2203	-0.2266	0.7575	0.1621	-0.0035	0.148	-0.3804	-0.0186	0.2134	0.1747	-0.0521	-0.0406	0.2512	-0.1145	0.2579	26.1162	9.9773	43.7026
12	2.658	1.7483	-0.1954	3.4674	-0.3199	3.031	0.1	-0.7126	0.1195	0.7018	-0.0781	-0.5663	-0.0513	0.1247	-0.0394	0.2767	0.0744	-0.0741	0.3502	-0.1165	0.203	25.4428	2.0445	54.7892
13	4.5132	1.1569	0.4786	1.5757	-0.4649	2.6164	-0.2531	-0.3019	0.6188	-0.1664	0.1217	0.0572	-0.4446	-0.1466	0.1567	0.1769	0.0264	-0.0269	0.2975	-0.0141	0.347	-2.5002	5.1709	37.0587
14	2.0252	0.9246	0.9013	0.5763	0.0722	1.1468	0.017	0.1428	-0.2534	-0.2862	0.2302	-0.0641	0.1118	0.0759	-0.1281	0.6117	-0.1865	-0.2451	0.317	-0.0461	0.5333	-10.873	-14.5227	29.4279
15	8.3278	1.5495	4.4495	2.0717	0.2305	6.6048	0.0331	-0.6696	-0.1633	0.6461	0.0892	-0.3243	0.4684	-0.1498	-0.1977	0.3173	0.0649	-0.0223	0.7655	0.0372	0.3537	-19.2276	-11.6556	28.0449
16	0.577	0.6731	-0.7965	3.6851	0.3318	1.6449	-0.0233	0.7824	0.1463	0.0378	0.086	-0.088	0.1892	0.5378	0.0241	0.1694	0.0638	-0.0337	0.5761	0.0488	0.2	-12.1008	-0.7005	44.0695
17	3.8586	1.4821	1.4985	4.752	1.8958	5.8831	0.0216	-0.7586	-0.8448	0.425	0.1342	0.5492	0.3247	-0.4334	-0.1296	0.3822	-0.0236	0.0047	0.4562	0.2057	0.5782	-8.2093	-12.2515	46.7038
18	5.7852	6.6527	1.706	8.9159	2.0187	2.6831	0.1475	-0.6035	-0.6712	0.4232	0.2516	-0.4252	0.2959	-0.3621	-0.2905	0.3081	0.0566	-0.0371	0.3724	0.0777	0.2438	-1.8263	-9.9369	46.1025
19	4.4582	0.7654	0.9031	6.5445	-0.1448	3.1942	0.1692	-0.2144	-0.7938	-0.0562	-0.0785	-0.0363	0.2889	-0.1055	-0.0726	0.2006	-0.0213	-0.0744	0.3832	0.0512	0.3243	-1.3268	-9.451	39.7833
20	5.4955	-2.7092	-0.4076	7.0225	1.8635	5.0512	0.189	0.7889	0.1378	-0.9477	-0.0897	0.202	0.0912	0.4422	-0.1074	0.3123	-0.0455	-0.1292	0.3143	0.0627	0.2304	-4.2187	-2.413	31.9257
21	5.8797	1.896	2.1826	4.1795	0.5112	0.8204	-0.3374	-0.1127	-0.6297	-0.3332	-0.462	0.0589	0.0408	-0.7677	0.4475	0.2357	-0.0423	-0.0412	0.6596	0.013	0.4142	-22.521	-7.7761	11.5116
22	1.554	-0.5449	1.4485	6.2869	-5.4662	5.3824	-0.2026	0.3762	-0.0203	-0.9473	0.1423	-0.17	0.923	0.5934	-0.0291	0.3826	0.0461	0.0247	0.6477	0.008	0.1707	-7.6762	-4.5134	0.7733
23	3.9464	4.1722	1.8983	7.6774	2.0875	2.8567	-0.0176	0.8272	0.4471	-0.391	0.4676	-0.4092	-0.3152	0.0453	-0.3278	0.2199	-0.0783	0.0253	0.5269	0.2763	0.6806	-7.5481	12.2835	-2.0587
24	9.4577	-5.9186	-3.522	4.1773	1.3196	3.2371	-0.1291	-0.2144	1.8638	0.1892	1.5852	-0.0566	-0.8005	-0.0822	-1.3853	0.4635	-0.0079	0.1265	0.6926	0.0693	0.6046	0.8446	10.8869	-1.775
25	6.158	0.3017	-4.6383	3.2933	-0.8664	4.8973	-0.0341	-0.6241	0.1644	-0.1489	0.2898	0.169	0.1254	-0.4921	-0.054	0.1966	-0.0224	-0.0919	0.6607	0.0335	0.2332	-7.9495	-3.3169	12.1395
26	6.5743	0.2562	-4.1509	1.0425	0.4452	6.344	0.1464	0.0624	-0.1838	0.1198	0.01	-0.1343	0.1756	0.0408	-0.2522	0.2001	-0.0416	-0.0427	0.6311	-0.1223	0.2206	-5.4658	-0.3006	13.8304
27	4.2865	0.2961	-5.442	0.8287	-0.4887	6.9266	-0.1243	-0.3981	0.1778	-0.0209	0.0374	0.0616	0.0677	-0.2379	0.0958	0.2517	-0.0092	-0.027	0.4872	-0.0539	0.2023	-3.1199	3.3561	14.0207
28	6.0607	3.2973	-1.6193	1.9574	-1.8701	8.3618	0.2463	-1.1564	0.6675	0.6144	-0.7154	-0.1926	-0.879	1.2246	0.3457	0.3464	-0.0761	-0.0005	0.3711	0.0435	0.4394	-9.0327	11.0797	15.7293
29	3.795	2.5763	-2.5624	2.1839	-2.2746	6.0173	0.2239	-0.9901	0.9019	0.326	0.0601	0.5638	-0.5897	-0.2271	-0.1679	0.2199	0.1079	0.0678	0.4196	-0.0532	0.366	-15.6935	8.995	15.022
30	4.0177	3.733	-0.64	3.6308	-1.3869	3.9569	-0.0207	-0.5024	0.5296	0.1352	-0.154	0.4908	-0.4028	-0.7369	0.1879	0.2409	0.0387	0.0058	0.3873	-0.0367	0.2942	-16.5436	9.3559	10.7513
31	3.9564	-0.4469	-0.7176	7.6997	-0.8848	4.5025	-0.004	0.5181	0.3742	-0.4712	-0.0216	0.7157	0.1371	-0.346	0.0663	0.1594	-0.0314	-0.007	0.2602	0.0737	0.2231	-15.3324	4.7905	4.4428
32	4.0917	-3.7777	2.8926	4.3485	-4.1659	4.6423	0.0933	0.0123	0.0609	-0.6786	0.1496	-0.0388	0.4517	-0.3708	-0.2602	0.2962	-0.001	0.0062	0.43	0.0089	0.1913	-11.6692	1.7974	0.1138

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq -3:28)	A	-3 - 28
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 29:47)	A	29 - 47
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 48:56)	A	48 - 56
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 57:67)	A	57 - 67
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 68:89)	A	68 - 89
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 90:111)	A	90 - 111
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 112:133)	A	112 - 133
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq -3:16)	B	-3 - 16
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 17:37)	B	17 - 37
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 38:67)	B	38 - 67
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 68:111)	B	68 - 111
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 112:133)	B	112 - 133
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq -3:16)	C	-3 - 16
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 17:28)	C	17 - 28
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 29:37)	C	29 - 37
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 38:67)	C	38 - 67
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 68:80)	C	68 - 80
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 81:89)	C	81 - 89
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 90:111)	C	90 - 111
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 112:133)	C	112 - 133
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq -3:7)	D	-3 - 7
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 8:16)	D	8 - 16
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 17:25)	D	17 - 25
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 26:37)	D	26 - 37
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 38:49)	D	38 - 49
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 50:57)	D	50 - 57
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 58:67)	D	58 - 67
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 68:80)	D	68 - 80
29	X-RAY DIFFRACTION	29	chain 'D' and (resseq 81:89)	D	81 - 89
30	X-RAY DIFFRACTION	30	chain 'D' and (resseq 90:99)	D	90 - 99
31	X-RAY DIFFRACTION	31	chain 'D' and (resseq 100:121)	D	100 - 121
32	X-RAY DIFFRACTION	32	chain 'D' and (resseq 122:133)	D	122 - 133

-
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

-
Group deposition

-
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

-Group deposition

-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

-
Group deposition

-
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