PDB-3s51: Structure of FANCI

ID or keywords:

Entry

Database: PDB / ID: 3s51

Title

Structure of FANCI

Components

Fanconi anemia group I protein homolog

Keywords

DNA BINDING PROTEIN /

dna repair

Function / homology

Function and homology information

Fanconi Anemia Pathway /

DNA repair complex /

DNA polymerase binding / positive regulation of protein ubiquitination /

cell cycle /

DNA repair /

nucleoplasm /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 3.3 Å

Authors

Pavletich, N.P.

Citation

Journal: Science / Year: 2011
Title: Structure of the FANCI-FANCD2 complex: insights into the Fanconi anemia DNA repair pathway.
Authors: Joo, W. / Xu, G. / Persky, N.S. / Smogorzewska, A. / Rudge, D.G. / Buzovetsky, O. / Elledge, S.J. / Pavletich, N.P.

History

Deposition	May 20, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2012	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3s51.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb3s51.ent.gz	1.5 MB	Display	PDB format
PDBx/mmJSON format	3s51.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/3s51 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/3s51	HTTPS FTP

-
Related structure data

Related structure data	3s4wC 3s4zC C: citing same article (ref.)
Similar structure data	3s4z-1 3s4z-2 3s4z-3 1eo8-d 1qfu-d 3k38-1 4idv-d 4lqq-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3s4wC

3s4zC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fanconi anemia group I protein homolog

B: Fanconi anemia group I protein homolog

C: Fanconi anemia group I protein homolog

D: Fanconi anemia group I protein homolog

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

1

A: Fanconi anemia group I protein homolog

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

2

B: Fanconi anemia group I protein homolog

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

3

C: Fanconi anemia group I protein homolog

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

4

D: Fanconi anemia group I protein homolog

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

5

A: Fanconi anemia group I protein homolog

B: Fanconi anemia group I protein homolog

defined by software
294 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

C: Fanconi anemia group I protein homolog

D: Fanconi anemia group I protein homolog

defined by software
294 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	114.700, 136.500, 149.700
Angle α, β, γ (deg.)	115.90, 106.00, 95.00
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13

#1: Protein	Fanconi anemia group I protein homolog / Protein FACI Mass: 147120.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fanci / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8K368

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.34 Å³/Da / Density % sol: 63.2 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 40 mM tri-potassium citrate, 10 % (w/v) polyethylene glycol (PEG) 3350, 10 mM EDTA, and 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 3.3→40 Å / Num. all: 114884 / Num. obs: 110174 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / R_merge(I) obs: 0.056 / Net I/σ(I): 23.1
Reflection shell	Resolution: 3.3→3.42 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.554 / Mean I/σ(I) obs: 1.4 / % possible all: 80.3

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHARP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-2000		data reduction
DPS		data reduction

Refinement

Method to determine structure:

MIRAS / Resolution: 3.3→39.82 Å / SU ML: 1.26 / σ(F): 0.04 / Phase error: 33.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2778	1943	2.01 %
R_work	0.2586	-	-
obs	0.259	96873	82.82 %
all	-	116958	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 124.688 Å² / k_sol: 0.303 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	38.0544 Å²	15.0049 Å²	26.8889 Å²
2-	-	-2.3641 Å²	-29.9743 Å²
3-	-	-	-35.6903 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→39.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34594	0	0	0	34594

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	35141
X-RAY DIFFRACTION	f_angle_d	0.869	47452
X-RAY DIFFRACTION	f_dihedral_angle_d	17.148	13148
X-RAY DIFFRACTION	f_chiral_restr	0.065	5719
X-RAY DIFFRACTION	f_plane_restr	0.004	5887

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	473	X-RAY DIFFRACTION	POSITIONAL
1	2	C	473	X-RAY DIFFRACTION	POSITIONAL	0.005
2	1	A	300	X-RAY DIFFRACTION	POSITIONAL
2	2	B	300	X-RAY DIFFRACTION	POSITIONAL	0.031
2	3	C	300	X-RAY DIFFRACTION	POSITIONAL	0.01
3	1	A	1182	X-RAY DIFFRACTION	POSITIONAL
3	2	B	1182	X-RAY DIFFRACTION	POSITIONAL	0.025
3	3	C	1182	X-RAY DIFFRACTION	POSITIONAL	0.018
3	4	D	1182	X-RAY DIFFRACTION	POSITIONAL	0.02
4	1	A	1138	X-RAY DIFFRACTION	POSITIONAL
4	2	B	1138	X-RAY DIFFRACTION	POSITIONAL	0.012
4	3	C	1138	X-RAY DIFFRACTION	POSITIONAL	0.082
4	4	D	1138	X-RAY DIFFRACTION	POSITIONAL	0.082
5	1	A	1132	X-RAY DIFFRACTION	POSITIONAL
5	2	B	1132	X-RAY DIFFRACTION	POSITIONAL	0.104
5	3	C	1132	X-RAY DIFFRACTION	POSITIONAL	0.01
5	4	D	1132	X-RAY DIFFRACTION	POSITIONAL	0.103
6	1	A	1166	X-RAY DIFFRACTION	POSITIONAL
6	2	B	1166	X-RAY DIFFRACTION	POSITIONAL	0.018
6	3	C	1166	X-RAY DIFFRACTION	POSITIONAL	0.019
6	4	D	1166	X-RAY DIFFRACTION	POSITIONAL	0.009
7	1	A	428	X-RAY DIFFRACTION	POSITIONAL
7	2	B	428	X-RAY DIFFRACTION	POSITIONAL	0.008
7	3	C	428	X-RAY DIFFRACTION	POSITIONAL	0.007
7	4	D	428	X-RAY DIFFRACTION	POSITIONAL	0.006
8	1	A	974	X-RAY DIFFRACTION	POSITIONAL
8	2	B	974	X-RAY DIFFRACTION	POSITIONAL	0.006
8	3	C	974	X-RAY DIFFRACTION	POSITIONAL	0.004
8	4	D	974	X-RAY DIFFRACTION	POSITIONAL	0.005
9	1	A	508	X-RAY DIFFRACTION	POSITIONAL
9	2	B	508	X-RAY DIFFRACTION	POSITIONAL	0.121
9	3	C	508	X-RAY DIFFRACTION	POSITIONAL	0.009
9	4	D	508	X-RAY DIFFRACTION	POSITIONAL	0.01
10	1	A	655	X-RAY DIFFRACTION	POSITIONAL
10	2	B	655	X-RAY DIFFRACTION	POSITIONAL	0.009
10	3	C	655	X-RAY DIFFRACTION	POSITIONAL	0.009
10	4	D	655	X-RAY DIFFRACTION	POSITIONAL	0.009
11	1	A	477	X-RAY DIFFRACTION	POSITIONAL
11	2	B	477	X-RAY DIFFRACTION	POSITIONAL	0.005
11	3	C	477	X-RAY DIFFRACTION	POSITIONAL	0.006
11	4	D	477	X-RAY DIFFRACTION	POSITIONAL	0.005
12	1	A	252	X-RAY DIFFRACTION	POSITIONAL
12	2	B	252	X-RAY DIFFRACTION	POSITIONAL	0.006
12	3	C	252	X-RAY DIFFRACTION	POSITIONAL	0.006
12	4	D	252	X-RAY DIFFRACTION	POSITIONAL	0.006
13	1	A	275	X-RAY DIFFRACTION	POSITIONAL
13	2	B	275	X-RAY DIFFRACTION	POSITIONAL	0.004
13	3	C	275	X-RAY DIFFRACTION	POSITIONAL	0.005
13	4	D	275	X-RAY DIFFRACTION	POSITIONAL	0.004

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.2779-3.3598	0.4436	61	0.4268	3187	X-RAY DIFFRACTION	39
3.3598-3.4506	0.437	92	0.3974	5011	X-RAY DIFFRACTION	61
3.4506-3.5521	0.4256	118	0.3765	5729	X-RAY DIFFRACTION	70
3.5521-3.6666	0.3899	126	0.3517	6129	X-RAY DIFFRACTION	75
3.6666-3.7976	0.2849	116	0.3149	6589	X-RAY DIFFRACTION	80
3.7976-3.9495	0.3139	159	0.2771	6818	X-RAY DIFFRACTION	84
3.9495-4.1291	0.2527	151	0.2482	7152	X-RAY DIFFRACTION	87
4.1291-4.3465	0.2703	163	0.2288	7386	X-RAY DIFFRACTION	91
4.3465-4.6185	0.2364	165	0.2125	7687	X-RAY DIFFRACTION	94
4.6185-4.9744	0.2719	155	0.2308	7693	X-RAY DIFFRACTION	94
4.9744-5.4739	0.3288	172	0.2807	7879	X-RAY DIFFRACTION	96
5.4739-6.2633	0.3681	146	0.3174	7870	X-RAY DIFFRACTION	96
6.2633-7.8811	0.2662	139	0.2643	7903	X-RAY DIFFRACTION	96
7.8811-39.8224	0.2167	180	0.2099	7897	X-RAY DIFFRACTION	97

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	1.0479	0.1326	1.9978	1.193	1.2761	2.9912	-0.4027	0.2362	-0.224	-0.6375	0.0027	0.7296	-0.3354	-0.4716	0.0041	1.2234	0.0775	0.0357	1.7392	-0.5593	1.4796	13.3374	-66.2517	-34.8804
2	4.1822	1.1139	-0.9651	2.0482	0.5663	1.9468	-0.1625	0.3931	-0.1815	-0.0374	-0.4021	-0.0469	0.0208	-0.0677	-0.0004	1.2121	0.0825	0.433	1.2589	-0.0906	1.1205	22.6421	-50.7887	-4.1266
3	1.8562	-0.6828	-0.9598	5.7117	1.8689	3.438	-0.3971	-0.176	-0.0941	-0.1794	-0.0486	-0.4732	0.4417	0.1446	-0.0017	0.596	-0.0542	0.2534	0.7309	0.0554	1.0061	21.6256	-43.0521	16.2845
4	1.8625	-0.6272	0.5075	3.6082	1.0495	1.7073	-0.29	0.1091	0.1088	-0.2091	0.176	0.0245	-0.2312	0.1501	0.0001	0.5982	-0.0823	-0.0516	0.8638	-0.0785	1.001	9.2103	-22.5434	32.953
5	2.5669	-1.8333	0.9341	2.7404	2.249	1.7758	-0.0278	-0.3341	0.6512	0.486	0.5801	-0.6847	-0.9837	0.3798	0.1945	0.5076	-0.3071	-0.3494	1.0706	-0.2367	1.0572	19.1826	-11.7472	50.8256
6	2.3285	0.972	0.5215	0.2788	1.5984	3.8361	-0.0682	-0.3334	-0.2186	-0.0449	0.2009	-1.2028	0.4401	0.6795	0.0036	0.8842	0.0785	-0.151	1.4933	0.1565	1.999	43.9853	-27.4232	47.8866
7	0.414	0.6634	0.0587	1.1532	1.3655	3.6338	1.2385	0.0717	0.8501	0.4812	-0.0158	-0.8589	2.3506	1.0712	0.0586	0.6422	0.1162	0.0405	1.9786	0.223	3.0173	56.8242	-53.0014	33.0842
8	0.7227	1.5725	1.0808	1.3536	1.2413	0.5491	0.3083	-0.3753	-0.2773	0.7213	-0.1444	-0.6897	0.4213	-1.0078	0.0003	1.4935	0.5202	-0.076	1.6667	-0.0925	2.476	47.219	-68.0867	26.6406
9	0.4724	0.0773	-0.3621	0.3635	0.6856	0.5501	1.1679	-0.6094	-1.4899	0.4752	-0.1416	-2.6099	2.2389	1.8266	0.0057	2.8949	0.0247	-0.4575	1.5843	0.1468	2.8196	46.6694	-81.6111	24.5558
10	3.7357	-1.5835	0.075	0.8786	-0.9294	1.924	-0.41	-0.8854	1.3593	1.3377	0.3762	-0.2739	-1.4998	0.9794	-0.0005	2.5944	-0.5806	-0.4378	1.5099	0.0186	2.107	28.8417	26.1592	37.3039
11	1.6916	0.4048	0.3686	3.1039	-0.0258	2.6123	-0.0747	0.3349	0.3397	-0.1293	-0.1109	-0.2908	-1.3827	-0.0796	-0	1.4063	-0.1763	-0.0931	0.9562	-0.0083	1.5001	10.3161	12.6479	16.8385
12	1.9647	0.8361	-1.0609	3.2954	1.0046	2.4534	-0.2077	0.4778	0.3464	-0.4057	0.2197	-0.404	-0.557	0.1158	0.0017	1.1636	-0.2311	0.1801	0.9095	0.1367	1.2924	5.8554	2.3427	6.9622
13	0.6794	0.7115	0.7133	5.136	1.0758	2.0894	-0.0459	0.4278	0.1476	-0.4738	0.1927	0.0384	0.0006	-0.0229	0.0002	1.1285	-0.0629	0.0289	0.8379	0.1542	0.8423	-4.7519	-20.4675	3.3831
14	1.5705	0.6153	1.6252	2.5408	-1.6186	4.6868	-0.1457	0.8705	-0.5582	-1.3138	0.4334	-0.0621	0.4156	0.3575	-0.0001	1.7647	-0.1839	0.0459	1.3064	-0.1352	0.8581	-10.1395	-32.8086	-17.4267
15	0.5444	1.4245	1.1149	1.1197	0.9518	2.8069	-0.0115	0.4379	0.1757	-1.2369	0.294	-0.3742	-0.6263	-0.045	0.0003	2.4107	-0.1392	0.3157	1.6259	0.2103	1.4591	-1.3198	-0.9174	-30.6701
16	0.9357	-0.7921	-0.8201	1.3464	1.6259	1.6647	-0.155	-0.3233	-0.0023	-0.4064	-0.0985	0.0845	-0.9004	-1.0573	-0.0073	2.8942	0.1031	-0.0513	1.0302	0.5279	1.676	-2.518	33.421	-11.7432
17	0.4184	0.7345	-0.2749	0.4818	-0.1812	-0.1051	0.236	-0.2679	0.9662	-0.8875	-0.0777	-0.7134	-3.1715	-1.1312	0.0231	2.9931	0.7274	-0.0179	1.6	0.0269	2.4165	-6.8111	45.3973	-6.7429
18	-0.1442	1.172	0.3015	3.4039	0.9377	-0.1428	0.1278	-0.5001	1.0462	-1.0033	-0.276	-0.0768	-0.7172	0.5378	-0.0086	2.3633	-0.2392	0.2837	1.5592	-0.2999	1.5892	-17.6395	15.4165	84.5502
19	1.1153	1.3617	0.6753	3.5598	-0.1803	2.0008	0.0292	-0.2426	0.0897	-0.0527	-0.0894	-0.0319	-0.2013	-0.1291	0	1.141	0.1765	0.1582	1.4566	-0.0459	0.9911	-18.6467	-13.2495	74.5214
20	3.4143	0.1486	-0.3787	4.9704	1.1493	4.5561	-0.0338	-0.2483	-0.1784	0.4723	0.0755	-0.2177	-0.199	0.2607	0.0001	0.622	0.2044	-0.0383	1.2569	-0.0641	0.6939	-10.4437	-27.5209	61.4979
21	1.6507	0.2113	0.4056	2.3134	1.3027	4.2597	-0.3565	-0.3112	-0.0927	0.7064	0.1332	0.1386	0.6699	-0.0363	-0.0003	0.7478	-0.0277	-0.0177	1.0107	0.0313	0.8041	-11.3821	-37.5237	50.3632
22	2.4425	1.007	0.7359	3.567	2.1399	3.5128	-0.3876	-0.2364	-0.3482	-0.2868	0.1449	0.0467	0.3819	-0.0379	-0.0006	0.6938	-0.0779	0.0352	0.6553	0.1438	0.6895	-7.8639	-42.2842	25.5743
23	-0.1552	0.5515	-0.3812	4.4812	-0.5713	5.2018	0.1093	0.6004	-0.5855	-0.4579	-0.074	0.3219	1.0853	-0.394	-0.0013	1.3172	-0.3475	0.0002	0.8974	-0.135	1.292	-11.2653	-62.8577	12.3788
24	-0.3152	0.4535	-0.0027	3.6264	1.0528	2.6594	-0.0879	-0.5641	-0.1458	0.416	-0.0728	0.1175	0.4756	-0.1013	0	1.6478	-0.0915	0.0742	1.2299	0.1969	1.4911	-16.2239	-76.0828	38.4946
25	1.339	0.8697	-0.0443	1.2093	1.2137	1.4416	-0.2554	0.33	-0.1311	1.8838	-0.1989	0.6894	1.8395	-0.0495	-0.0388	2.6723	-0.1259	0.2761	1.7791	0.5793	1.5408	-13.3158	-71.8169	70.3172
26	3.1486	0.8676	0.9082	0.2717	0.4246	-0.1416	0.0004	-0.111	-0.0831	0.5451	0.7863	-1.782	0.0648	0.7798	0.0628	3.962	0.1304	0.0401	1.1752	1.47	-0.8647	-1.4928	-59.527	78.8012
27	0.5051	-0.0906	0.1541	-0.2221	-0.0085	0.0526	-0.2707	-1.2499	0.0621	3.1044	0.2246	-0.7309	1.7651	-0.3087	0.0154	2.8321	0.2056	-0.6011	1.9891	0.4682	1.6433	6.6351	-56.5751	89.3576
28	0.4315	-0.3619	0.0583	0.1823	-0.3012	0.2329	0.0667	3.275	-1.5341	0.4316	-0.2012	-0.1184	2.2382	-0.8829	-0.0014	2.5704	-0.5154	-0.4747	3.19	-0.7675	2.7277	-50.4267	-61.6683	-10.0145
29	3.1701	0.0433	0.6528	3.5075	0.0076	2.8518	0.0096	0.9107	-0.7376	-0.4649	0.2545	0.8174	0.0508	-0.885	0.0001	1.0541	-0.3604	-0.2946	1.7711	0.0576	1.2933	-41.2547	-36.6219	3.2213
30	1.5135	0.2113	1.5861	0.6031	0.1127	2.3828	-0.01	0.19	0.0927	-0.103	0.1157	0.4854	-0.0832	-0.6276	0.0002	0.8124	0.012	-0.0753	1.5262	0.1539	1.0951	-35.2467	-21.6296	11.976
31	2.1386	0.9783	2.9727	1.5994	1.9637	3.742	-0.1734	0.2922	0.3449	-0.1096	0.3203	0.055	-0.3169	-0.5025	0.0002	0.6591	0.2371	-0.1095	1.0239	0.053	0.914	-16.3523	-10.9352	25.2144
32	3.4699	-2.0711	1.501	2.8191	-0.1464	-0.1912	-0.2438	-0.6638	0.8327	0.5502	0.1679	0.0448	-0.6129	-0.3573	0.0002	1.4192	0.3431	0.0052	1.0953	-0.255	1.1649	-16.0079	8.8702	40.0577
33	1.394	0.1243	0.4126	2.491	0.8499	-0.3329	-0.1176	-0.4917	0.3481	-0.1167	0.0591	0.3551	-0.6361	-0.8229	0.0006	1.2326	0.4755	-0.1916	1.8892	0.2717	1.5944	-49.8085	10.2584	22.6851
34	2.214	1.1793	-1.7247	0.2608	-0.3295	1.2357	0.2758	0.3032	0.0957	-1.6687	-0.6891	0.4006	-0.588	-0.9886	0.0002	2.1888	0.3684	-0.699	2.1975	0.2779	1.6981	-62.9564	-5.8609	-16.4156

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:204)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 205:306)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 307:469)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 470:545)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 546:732)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 733:991)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 992:1053)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 1054:1186)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 1187:1280)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 64:248)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 249:344)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 345:450)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 451:545)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 546:732)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 733:1053)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 1054:1186)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 1187:1280)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 1:152)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 153:248)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 249:344)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 345:450)
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 451:545)
23	X-RAY DIFFRACTION	23	chain 'C' and (resseq 546:732)
24	X-RAY DIFFRACTION	24	chain 'C' and (resseq 733:991)
25	X-RAY DIFFRACTION	25	chain 'C' and (resseq 992:1053)
26	X-RAY DIFFRACTION	26	chain 'C' and (resseq 1054:1186)
27	X-RAY DIFFRACTION	27	chain 'C' and (resseq 1187:1280)
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 101:204)
29	X-RAY DIFFRACTION	29	chain 'D' and (resseq 205:344)
30	X-RAY DIFFRACTION	30	chain 'D' and (resseq 345:450)
31	X-RAY DIFFRACTION	31	chain 'D' and (resseq 451:545)
32	X-RAY DIFFRACTION	32	chain 'D' and (resseq 546:732)
33	X-RAY DIFFRACTION	33	chain 'D' and (resseq 733:1104)
34	X-RAY DIFFRACTION	34	chain 'D' and (resseq 1105:1280)

-
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