PDB-6txe: Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626...

ID or keywords:

Entry

Database: PDB / ID: 6txe

Title

Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dTMPNPP and Mg

Components

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

Keywords

HYDROLASE / triphosphohydrolase / metallo-enzyme / binuclear / HD

Function / homology

Function and homology information

Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.19 Å

Authors

Morris, E.R. / Kunzelmann, S. / Caswell, S.J. / Arnold, L.H. / Purkiss, A.G. / Kelly, G. / Taylor, I.A.

Funding support

United Kingdom, 4items

Organization	Grant number	Country
Wellcome Trust	108014/Z/15/Z	United Kingdom
Wellcome Trust	FC001029	United Kingdom
Medical Research Council (MRC, United Kingdom)	FC001029	United Kingdom
Cancer Research UK	FC001029	United Kingdom

Citation

Journal: Nat Commun / Year: 2020
Title: Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis.
Authors: Morris, E.R. / Caswell, S.J. / Kunzelmann, S. / Arnold, L.H. / Purkiss, A.G. / Kelly, G. / Taylor, I.A.

History

Deposition	Jan 14, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 24, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 8, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6txe.cif.gz	3 MB	Display	PDBx/mmCIF format
PDB format	pdb6txe.ent.gz	2.5 MB	Display	PDB format
PDBx/mmJSON format	6txe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6txe_validation.pdf.gz	25.2 MB	Display	wwPDB validaton report
Full document	6txe_full_validation.pdf.gz	25.4 MB	Display
Data in XML	6txe_validation.xml.gz	259.1 KB	Display
Data in CIF	6txe_validation.cif.gz	338.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/6txe ftp://data.pdbj.org/pub/pdb/validation_reports/tx/6txe	HTTPS FTP

-
Related structure data

Related structure data	6tx0C 6txaSC 6txcC 6txfC 6xu1C 6yomC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6txc-3 4to5-d 4tnq-d 6dwd-d 6txa-4 4bzb-d 6xu1-2 4tny-d 4to6-d 6dw7-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6txaSC

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#238 - Oct 2019 Ribonucleotide Reductase similarity (1) #177 - Sep 2014 Apoptosomes similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2)

Deposited unit

A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

I: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

J: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

K: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

L: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

M: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

N: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

O: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

P: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

hetero molecules

990 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

hetero molecules

defined by author&software
Evidence: assay for oligomerization, SEC-MALLS and AUC experiments demonstrate the HD domain crystallised here assembles into a homotetramer in the presence of GTP, dATP, dTMPNPP and Mg2+.
248 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

hetero molecules

defined by author&software
248 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

J: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

K: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

L: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

hetero molecules

defined by author&software
248 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

M: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

N: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

O: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

P: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

hetero molecules

defined by author&software
247 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.482, 172.232, 275.271
Angle α, β, γ (deg.)	90.000, 95.310, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	ASN	ASN	A	A	114 - 599	8 - 493
2	1	THR	THR	ASN	ASN	B	B	114 - 599	8 - 493
1	2	MET	MET	ASN	ASN	A	A	115 - 599	9 - 493
2	2	MET	MET	ASN	ASN	C	C	115 - 599	9 - 493
1	3	THR	THR	ASN	ASN	A	A	114 - 599	8 - 493
2	3	THR	THR	ASN	ASN	D	D	114 - 599	8 - 493
1	4	THR	THR	ASN	ASN	A	A	114 - 599	8 - 493
2	4	THR	THR	ASN	ASN	E	E	114 - 599	8 - 493
1	5	THR	THR	TRP	TRP	A	A	114 - 598	8 - 492
2	5	THR	THR	TRP	TRP	F	F	114 - 598	8 - 492
1	6	THR	THR	GLU	GLU	A	A	114 - 597	8 - 491
2	6	THR	THR	GLU	GLU	G	G	114 - 597	8 - 491
1	7	THR	THR	ASN	ASN	A	A	114 - 599	8 - 493
2	7	THR	THR	ASN	ASN	H	H	114 - 599	8 - 493
1	8	MET	MET	ASN	ASN	A	A	115 - 599	9 - 493
2	8	MET	MET	ASN	ASN	I	I	115 - 599	9 - 493
1	9	MET	MET	GLU	GLU	A	A	115 - 597	9 - 491
2	9	MET	MET	GLU	GLU	J	J	115 - 597	9 - 491
1	10	MET	MET	ASN	ASN	A	A	115 - 599	9 - 493
2	10	MET	MET	ASN	ASN	K	K	115 - 599	9 - 493
1	11	MET	MET	ASN	ASN	A	A	115 - 599	9 - 493
2	11	MET	MET	ASN	ASN	L	L	115 - 599	9 - 493
1	12	MET	MET	TRP	TRP	A	A	115 - 598	9 - 492
2	12	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	13	MET	MET	ASN	ASN	A	A	115 - 599	9 - 493
2	13	MET	MET	ASN	ASN	N	N	115 - 599	9 - 493
1	14	THR	THR	GLN	GLN	A	A	114 - 594	8 - 488
2	14	THR	THR	GLN	GLN	O	O	114 - 594	8 - 488
1	15	THR	THR	PRO	PRO	A	A	114 - 593	8 - 487
2	15	THR	THR	PRO	PRO	P	P	114 - 593	8 - 487
1	16	MET	MET	ASN	ASN	B	B	115 - 599	9 - 493
2	16	MET	MET	ASN	ASN	C	C	115 - 599	9 - 493
1	17	THR	THR	ASN	ASN	B	B	114 - 599	8 - 493
2	17	THR	THR	ASN	ASN	D	D	114 - 599	8 - 493
1	18	THR	THR	ASN	ASN	B	B	114 - 599	8 - 493
2	18	THR	THR	ASN	ASN	E	E	114 - 599	8 - 493
1	19	THR	THR	GLU	GLU	B	B	114 - 597	8 - 491
2	19	THR	THR	GLU	GLU	F	F	114 - 597	8 - 491
1	20	THR	THR	TRP	TRP	B	B	114 - 598	8 - 492
2	20	THR	THR	TRP	TRP	G	G	114 - 598	8 - 492
1	21	THR	THR	ASN	ASN	B	B	114 - 599	8 - 493
2	21	THR	THR	ASN	ASN	H	H	114 - 599	8 - 493
1	22	MET	MET	ASN	ASN	B	B	115 - 599	9 - 493
2	22	MET	MET	ASN	ASN	I	I	115 - 599	9 - 493
1	23	MET	MET	GLU	GLU	B	B	115 - 597	9 - 491
2	23	MET	MET	GLU	GLU	J	J	115 - 597	9 - 491
1	24	MET	MET	TRP	TRP	B	B	115 - 598	9 - 492
2	24	MET	MET	TRP	TRP	K	K	115 - 598	9 - 492
1	25	MET	MET	TRP	TRP	B	B	115 - 598	9 - 492
2	25	MET	MET	TRP	TRP	L	L	115 - 598	9 - 492
1	26	MET	MET	TRP	TRP	B	B	115 - 598	9 - 492
2	26	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	27	MET	MET	ASN	ASN	B	B	115 - 599	9 - 493
2	27	MET	MET	ASN	ASN	N	N	115 - 599	9 - 493
1	28	THR	THR	GLN	GLN	B	B	114 - 594	8 - 488
2	28	THR	THR	GLN	GLN	O	O	114 - 594	8 - 488
1	29	THR	THR	PRO	PRO	B	B	114 - 593	8 - 487
2	29	THR	THR	PRO	PRO	P	P	114 - 593	8 - 487
1	30	MET	MET	TRP	TRP	C	C	115 - 598	9 - 492
2	30	MET	MET	TRP	TRP	D	D	115 - 598	9 - 492
1	31	MET	MET	ASN	ASN	C	C	115 - 599	9 - 493
2	31	MET	MET	ASN	ASN	E	E	115 - 599	9 - 493
1	32	MET	MET	TRP	TRP	C	C	115 - 598	9 - 492
2	32	MET	MET	TRP	TRP	F	F	115 - 598	9 - 492
1	33	MET	MET	GLU	GLU	C	C	115 - 597	9 - 491
2	33	MET	MET	GLU	GLU	G	G	115 - 597	9 - 491
1	34	MET	MET	ASN	ASN	C	C	115 - 599	9 - 493
2	34	MET	MET	ASN	ASN	H	H	115 - 599	9 - 493
1	35	MET	MET	ASN	ASN	C	C	115 - 599	9 - 493
2	35	MET	MET	ASN	ASN	I	I	115 - 599	9 - 493
1	36	MET	MET	TRP	TRP	C	C	115 - 598	9 - 492
2	36	MET	MET	TRP	TRP	J	J	115 - 598	9 - 492
1	37	MET	MET	ASN	ASN	C	C	115 - 599	9 - 493
2	37	MET	MET	ASN	ASN	K	K	115 - 599	9 - 493
1	38	MET	MET	ASN	ASN	C	C	115 - 599	9 - 493
2	38	MET	MET	ASN	ASN	L	L	115 - 599	9 - 493
1	39	MET	MET	TRP	TRP	C	C	115 - 598	9 - 492
2	39	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	40	MET	MET	ASN	ASN	C	C	115 - 599	9 - 493
2	40	MET	MET	ASN	ASN	N	N	115 - 599	9 - 493
1	41	MET	MET	PRO	PRO	C	C	115 - 593	9 - 487
2	41	MET	MET	PRO	PRO	O	O	115 - 593	9 - 487
1	42	MET	MET	PRO	PRO	C	C	115 - 593	9 - 487
2	42	MET	MET	PRO	PRO	P	P	115 - 593	9 - 487
1	43	THR	THR	ASN	ASN	D	D	114 - 599	8 - 493
2	43	THR	THR	ASN	ASN	E	E	114 - 599	8 - 493
1	44	THR	THR	TRP	TRP	D	D	114 - 598	8 - 492
2	44	THR	THR	TRP	TRP	F	F	114 - 598	8 - 492
1	45	THR	THR	TRP	TRP	D	D	114 - 598	8 - 492
2	45	THR	THR	TRP	TRP	G	G	114 - 598	8 - 492
1	46	THR	THR	ASN	ASN	D	D	114 - 599	8 - 493
2	46	THR	THR	ASN	ASN	H	H	114 - 599	8 - 493
1	47	MET	MET	ASN	ASN	D	D	115 - 599	9 - 493
2	47	MET	MET	ASN	ASN	I	I	115 - 599	9 - 493
1	48	MET	MET	GLU	GLU	D	D	115 - 597	9 - 491
2	48	MET	MET	GLU	GLU	J	J	115 - 597	9 - 491
1	49	MET	MET	ASN	ASN	D	D	115 - 599	9 - 493
2	49	MET	MET	ASN	ASN	K	K	115 - 599	9 - 493
1	50	MET	MET	ASN	ASN	D	D	115 - 599	9 - 493
2	50	MET	MET	ASN	ASN	L	L	115 - 599	9 - 493
1	51	MET	MET	TRP	TRP	D	D	115 - 598	9 - 492
2	51	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	52	MET	MET	ASN	ASN	D	D	115 - 599	9 - 493
2	52	MET	MET	ASN	ASN	N	N	115 - 599	9 - 493
1	53	THR	THR	GLN	GLN	D	D	114 - 594	8 - 488
2	53	THR	THR	GLN	GLN	O	O	114 - 594	8 - 488
1	54	THR	THR	PRO	PRO	D	D	114 - 593	8 - 487
2	54	THR	THR	PRO	PRO	P	P	114 - 593	8 - 487
1	55	THR	THR	GLU	GLU	E	E	114 - 597	8 - 491
2	55	THR	THR	GLU	GLU	F	F	114 - 597	8 - 491
1	56	THR	THR	TRP	TRP	E	E	114 - 598	8 - 492
2	56	THR	THR	TRP	TRP	G	G	114 - 598	8 - 492
1	57	THR	THR	ASN	ASN	E	E	114 - 599	8 - 493
2	57	THR	THR	ASN	ASN	H	H	114 - 599	8 - 493
1	58	MET	MET	ASN	ASN	E	E	115 - 599	9 - 493
2	58	MET	MET	ASN	ASN	I	I	115 - 599	9 - 493
1	59	MET	MET	GLU	GLU	E	E	115 - 597	9 - 491
2	59	MET	MET	GLU	GLU	J	J	115 - 597	9 - 491
1	60	MET	MET	TRP	TRP	E	E	115 - 598	9 - 492
2	60	MET	MET	TRP	TRP	K	K	115 - 598	9 - 492
1	61	MET	MET	TRP	TRP	E	E	115 - 598	9 - 492
2	61	MET	MET	TRP	TRP	L	L	115 - 598	9 - 492
1	62	MET	MET	TRP	TRP	E	E	115 - 598	9 - 492
2	62	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	63	MET	MET	ASN	ASN	E	E	115 - 599	9 - 493
2	63	MET	MET	ASN	ASN	N	N	115 - 599	9 - 493
1	64	THR	THR	GLN	GLN	E	E	114 - 594	8 - 488
2	64	THR	THR	GLN	GLN	O	O	114 - 594	8 - 488
1	65	THR	THR	PRO	PRO	E	E	114 - 593	8 - 487
2	65	THR	THR	PRO	PRO	P	P	114 - 593	8 - 487
1	66	THR	THR	TRP	TRP	F	F	114 - 598	8 - 492
2	66	THR	THR	TRP	TRP	G	G	114 - 598	8 - 492
1	67	THR	THR	TRP	TRP	F	F	114 - 598	8 - 492
2	67	THR	THR	TRP	TRP	H	H	114 - 598	8 - 492
1	68	MET	MET	GLU	GLU	F	F	115 - 597	9 - 491
2	68	MET	MET	GLU	GLU	I	I	115 - 597	9 - 491
1	69	MET	MET	TRP	TRP	F	F	115 - 598	9 - 492
2	69	MET	MET	TRP	TRP	J	J	115 - 598	9 - 492
1	70	MET	MET	GLU	GLU	F	F	115 - 597	9 - 491
2	70	MET	MET	GLU	GLU	K	K	115 - 597	9 - 491
1	71	MET	MET	GLU	GLU	F	F	115 - 597	9 - 491
2	71	MET	MET	GLU	GLU	L	L	115 - 597	9 - 491
1	72	MET	MET	TRP	TRP	F	F	115 - 598	9 - 492
2	72	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	73	MET	MET	GLU	GLU	F	F	115 - 597	9 - 491
2	73	MET	MET	GLU	GLU	N	N	115 - 597	9 - 491
1	74	THR	THR	GLN	GLN	F	F	114 - 594	8 - 488
2	74	THR	THR	GLN	GLN	O	O	114 - 594	8 - 488
1	75	THR	THR	PRO	PRO	F	F	114 - 593	8 - 487
2	75	THR	THR	PRO	PRO	P	P	114 - 593	8 - 487
1	76	THR	THR	GLU	GLU	G	G	114 - 597	8 - 491
2	76	THR	THR	GLU	GLU	H	H	114 - 597	8 - 491
1	77	MET	MET	TRP	TRP	G	G	115 - 598	9 - 492
2	77	MET	MET	TRP	TRP	I	I	115 - 598	9 - 492
1	78	MET	MET	GLU	GLU	G	G	115 - 597	9 - 491
2	78	MET	MET	GLU	GLU	J	J	115 - 597	9 - 491
1	79	MET	MET	GLU	GLU	G	G	115 - 597	9 - 491
2	79	MET	MET	GLU	GLU	K	K	115 - 597	9 - 491
1	80	MET	MET	GLU	GLU	G	G	115 - 597	9 - 491
2	80	MET	MET	GLU	GLU	L	L	115 - 597	9 - 491
1	81	MET	MET	TRP	TRP	G	G	115 - 598	9 - 492
2	81	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	82	MET	MET	TRP	TRP	G	G	115 - 598	9 - 492
2	82	MET	MET	TRP	TRP	N	N	115 - 598	9 - 492
1	83	THR	THR	GLN	GLN	G	G	114 - 594	8 - 488
2	83	THR	THR	GLN	GLN	O	O	114 - 594	8 - 488
1	84	THR	THR	PRO	PRO	G	G	114 - 593	8 - 487
2	84	THR	THR	PRO	PRO	P	P	114 - 593	8 - 487
1	85	MET	MET	ASN	ASN	H	H	115 - 599	9 - 493
2	85	MET	MET	ASN	ASN	I	I	115 - 599	9 - 493
1	86	MET	MET	GLU	GLU	H	H	115 - 597	9 - 491
2	86	MET	MET	GLU	GLU	J	J	115 - 597	9 - 491
1	87	MET	MET	ASN	ASN	H	H	115 - 599	9 - 493
2	87	MET	MET	ASN	ASN	K	K	115 - 599	9 - 493
1	88	MET	MET	ASN	ASN	H	H	115 - 599	9 - 493
2	88	MET	MET	ASN	ASN	L	L	115 - 599	9 - 493
1	89	MET	MET	TRP	TRP	H	H	115 - 598	9 - 492
2	89	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	90	MET	MET	ASN	ASN	H	H	115 - 599	9 - 493
2	90	MET	MET	ASN	ASN	N	N	115 - 599	9 - 493
1	91	THR	THR	GLN	GLN	H	H	114 - 594	8 - 488
2	91	THR	THR	GLN	GLN	O	O	114 - 594	8 - 488
1	92	THR	THR	PRO	PRO	H	H	114 - 593	8 - 487
2	92	THR	THR	PRO	PRO	P	P	114 - 593	8 - 487
1	93	MET	MET	TRP	TRP	I	I	115 - 598	9 - 492
2	93	MET	MET	TRP	TRP	J	J	115 - 598	9 - 492
1	94	MET	MET	ASN	ASN	I	I	115 - 599	9 - 493
2	94	MET	MET	ASN	ASN	K	K	115 - 599	9 - 493
1	95	MET	MET	TRP	TRP	I	I	115 - 598	9 - 492
2	95	MET	MET	TRP	TRP	L	L	115 - 598	9 - 492
1	96	MET	MET	TRP	TRP	I	I	115 - 598	9 - 492
2	96	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	97	MET	MET	ASN	ASN	I	I	115 - 599	9 - 493
2	97	MET	MET	ASN	ASN	N	N	115 - 599	9 - 493
1	98	MET	MET	GLN	GLN	I	I	115 - 594	9 - 488
2	98	MET	MET	GLN	GLN	O	O	115 - 594	9 - 488
1	99	MET	MET	PRO	PRO	I	I	115 - 593	9 - 487
2	99	MET	MET	PRO	PRO	P	P	115 - 593	9 - 487
1	100	MET	MET	TRP	TRP	J	J	115 - 598	9 - 492
2	100	MET	MET	TRP	TRP	K	K	115 - 598	9 - 492
1	101	MET	MET	TRP	TRP	J	J	115 - 598	9 - 492
2	101	MET	MET	TRP	TRP	L	L	115 - 598	9 - 492
1	102	MET	MET	TRP	TRP	J	J	115 - 598	9 - 492
2	102	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	103	MET	MET	TRP	TRP	J	J	115 - 598	9 - 492
2	103	MET	MET	TRP	TRP	N	N	115 - 598	9 - 492
1	104	MET	MET	GLN	GLN	J	J	115 - 594	9 - 488
2	104	MET	MET	GLN	GLN	O	O	115 - 594	9 - 488
1	105	MET	MET	PRO	PRO	J	J	115 - 593	9 - 487
2	105	MET	MET	PRO	PRO	P	P	115 - 593	9 - 487
1	106	MET	MET	ASN	ASN	K	K	115 - 599	9 - 493
2	106	MET	MET	ASN	ASN	L	L	115 - 599	9 - 493
1	107	MET	MET	TRP	TRP	K	K	115 - 598	9 - 492
2	107	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
1	108	MET	MET	ASN	ASN	K	K	115 - 599	9 - 493
2	108	MET	MET	ASN	ASN	N	N	115 - 599	9 - 493
1	109	MET	MET	GLN	GLN	K	K	115 - 594	9 - 488
2	109	MET	MET	GLN	GLN	O	O	115 - 594	9 - 488
1	110	MET	MET	PRO	PRO	K	K	115 - 593	9 - 487
2	110	MET	MET	PRO	PRO	P	P	115 - 593	9 - 487
1	111	MET	MET	GLU	GLU	L	L	115 - 597	9 - 491
2	111	MET	MET	GLU	GLU	M	M	115 - 597	9 - 491
1	112	MET	MET	TRP	TRP	L	L	115 - 598	9 - 492
2	112	MET	MET	TRP	TRP	N	N	115 - 598	9 - 492
1	113	MET	MET	GLN	GLN	L	L	115 - 594	9 - 488
2	113	MET	MET	GLN	GLN	O	O	115 - 594	9 - 488
1	114	MET	MET	PRO	PRO	L	L	115 - 593	9 - 487
2	114	MET	MET	PRO	PRO	P	P	115 - 593	9 - 487
1	115	MET	MET	TRP	TRP	M	M	115 - 598	9 - 492
2	115	MET	MET	TRP	TRP	N	N	115 - 598	9 - 492
1	116	MET	MET	GLN	GLN	M	M	115 - 594	9 - 488
2	116	MET	MET	GLN	GLN	O	O	115 - 594	9 - 488
1	117	MET	MET	PRO	PRO	M	M	115 - 593	9 - 487
2	117	MET	MET	PRO	PRO	P	P	115 - 593	9 - 487
1	118	MET	MET	GLN	GLN	N	N	115 - 594	9 - 488
2	118	MET	MET	GLN	GLN	O	O	115 - 594	9 - 488
1	119	MET	MET	PRO	PRO	N	N	115 - 593	9 - 487
2	119	MET	MET	PRO	PRO	P	P	115 - 593	9 - 487
1	120	THR	THR	GLN	GLN	O	O	114 - 594	8 - 488
2	120	THR	THR	GLN	GLN	P	P	114 - 594	8 - 488

NCS ensembles :

-
Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM domain and HD domain-containing protein 1 / hSAMHD1 Mass: 60208.809 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases

#1: Protein

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...

Mass: 60208.809 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases

-
Non-polymers , 6 types, 107 molecules

#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-1FZ / 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine Mass: 481.184 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₁₀H₁₈N₃O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#6: Chemical	ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE Mass: 491.182 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M Bistris methane-HCl pH 6, 19% (w/v) PEG 3350, 0.15 M Li2SO4

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 3.186→91.364 Å / Num. obs: 80315 / % possible obs: 91.364 % / Redundancy: 7 % / B_iso Wilson estimate: 50.1 Å² / CC_1/2: 0.96 / R_merge(I) obs: 0.433 / R_pim(I) all: 0.175 / R_rim(I) all: 0.467 / Net I/σ(I): 4.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
3.186-3.63	6.7	1.161	1.7	4016	0.668	0.476	1.257	76.2
10.672-91.364	6.8	0.08	16.1	4014	0.996	0.033	0.087	96.7

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	9.52 Å	274.09 Å
Translation	9.52 Å	274.09 Å

-
Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.4	data scaling
STARANISO		data scaling
PHASER	2.7.17	phasing
REFMAC	5.8.0158	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6TXA

6txa

Resolution: 3.19→91.22 Å / Cor.coef. F_o:F_c: 0.874 / Cor.coef. F_o:F_c free: 0.798 / SU B: 78.217 / SU ML: 0.564 / SU R Cruickshank DPI: 0.7955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.914
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2518	4073	5.1 %	RANDOM
R_work	0.2179	-	-	-
obs	0.2196	76240	53.35 %	-

Solvent computation

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

Displacement parameters

B_iso max: 204 Å² / B_iso mean: 64.692 Å² / B_iso min: 15.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.33 Å²	0 Å²	0.62 Å²
2-	-	3.52 Å²	0 Å²
3-	-	-	-2.27 Å²

Refinement step

Cycle: final / Resolution: 3.19→91.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	61116	0	1559	0	62675
B_iso mean	-	-	50.73	-	-
Num. residues	-	-	-	-	7654

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	64182
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	57427
X-RAY DIFFRACTION	r_angle_refined_deg	1.411	1.972	87377
X-RAY DIFFRACTION	r_angle_other_deg	1.008	2.995	132956
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.502	5	7623
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.696	23.986	3096
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.018	15	10439
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.255	15	396
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	9398
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	70642
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	13306

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	31922	0.04
1	2	B	31922	0.04
2	1	A	31872	0.04
2	2	C	31872	0.04
3	1	A	31930	0.04
3	2	D	31930	0.04
4	1	A	31958	0.04
4	2	E	31958	0.04
5	1	A	31864	0.03
5	2	F	31864	0.03
6	1	A	31672	0.04
6	2	G	31672	0.04
7	1	A	31980	0.04
7	2	H	31980	0.04
8	1	A	31738	0.04
8	2	I	31738	0.04
9	1	A	31654	0.03
9	2	J	31654	0.03
10	1	A	31958	0.03
10	2	K	31958	0.03
11	1	A	31474	0.04
11	2	L	31474	0.04
12	1	A	31262	0.04
12	2	M	31262	0.04
13	1	A	31710	0.03
13	2	N	31710	0.03
14	1	A	31398	0.04
14	2	O	31398	0.04
15	1	A	31174	0.03
15	2	P	31174	0.03
16	1	B	31740	0.04
16	2	C	31740	0.04
17	1	B	31850	0.04
17	2	D	31850	0.04
18	1	B	31966	0.04
18	2	E	31966	0.04
19	1	B	31522	0.04
19	2	F	31522	0.04
20	1	B	31730	0.04
20	2	G	31730	0.04
21	1	B	31866	0.04
21	2	H	31866	0.04
22	1	B	31722	0.03
22	2	I	31722	0.03
23	1	B	31586	0.04
23	2	J	31586	0.04
24	1	B	31662	0.04
24	2	K	31662	0.04
25	1	B	31370	0.04
25	2	L	31370	0.04
26	1	B	31248	0.04
26	2	M	31248	0.04
27	1	B	31630	0.04
27	2	N	31630	0.04
28	1	B	31444	0.03
28	2	O	31444	0.03
29	1	B	31038	0.04
29	2	P	31038	0.04
30	1	C	31780	0.04
30	2	D	31780	0.04
31	1	C	31920	0.03
31	2	E	31920	0.03
32	1	C	31724	0.04
32	2	F	31724	0.04
33	1	C	31542	0.04
33	2	G	31542	0.04
34	1	C	31946	0.03
34	2	H	31946	0.03
35	1	C	31830	0.04
35	2	I	31830	0.04
36	1	C	31762	0.04
36	2	J	31762	0.04
37	1	C	31946	0.03
37	2	K	31946	0.03
38	1	C	31588	0.04
38	2	L	31588	0.04
39	1	C	31328	0.04
39	2	M	31328	0.04
40	1	C	31754	0.03
40	2	N	31754	0.03
41	1	C	31346	0.04
41	2	O	31346	0.04
42	1	C	31026	0.04
42	2	P	31026	0.04
43	1	D	31976	0.04
43	2	E	31976	0.04
44	1	D	31784	0.04
44	2	F	31784	0.04
45	1	D	31854	0.03
45	2	G	31854	0.03
46	1	D	31924	0.04
46	2	H	31924	0.04
47	1	D	31808	0.03
47	2	I	31808	0.03
48	1	D	31862	0.02
48	2	J	31862	0.02
49	1	D	31826	0.04
49	2	K	31826	0.04
50	1	D	31654	0.03
50	2	L	31654	0.03
51	1	D	31454	0.02
51	2	M	31454	0.02
52	1	D	31662	0.03
52	2	N	31662	0.03
53	1	D	31518	0.04
53	2	O	31518	0.04
54	1	D	31118	0.03
54	2	P	31118	0.03
55	1	E	31644	0.04
55	2	F	31644	0.04
56	1	E	31710	0.04
56	2	G	31710	0.04
57	1	E	31984	0.04
57	2	H	31984	0.04
58	1	E	31816	0.04
58	2	I	31816	0.04
59	1	E	31732	0.03
59	2	J	31732	0.03
60	1	E	31882	0.04
60	2	K	31882	0.04
61	1	E	31602	0.03
61	2	L	31602	0.03
62	1	E	31340	0.04
62	2	M	31340	0.04
63	1	E	31788	0.03
63	2	N	31788	0.03
64	1	E	31482	0.03
64	2	O	31482	0.03
65	1	E	31090	0.04
65	2	P	31090	0.04
66	1	F	31794	0.04
66	2	G	31794	0.04
67	1	F	31704	0.05
67	2	H	31704	0.05
68	1	F	31396	0.05
68	2	I	31396	0.05
69	1	F	31660	0.04
69	2	J	31660	0.04
70	1	F	31740	0.03
70	2	K	31740	0.03
71	1	F	31390	0.04
71	2	L	31390	0.04
72	1	F	31368	0.03
72	2	M	31368	0.03
73	1	F	31378	0.04
73	2	N	31378	0.04
74	1	F	31514	0.04
74	2	O	31514	0.04
75	1	F	31176	0.03
75	2	P	31176	0.03
76	1	G	31626	0.04
76	2	H	31626	0.04
77	1	G	31604	0.04
77	2	I	31604	0.04
78	1	G	31602	0.03
78	2	J	31602	0.03
79	1	G	31492	0.04
79	2	K	31492	0.04
80	1	G	31268	0.04
80	2	L	31268	0.04
81	1	G	31408	0.03
81	2	M	31408	0.03
82	1	G	31492	0.04
82	2	N	31492	0.04
83	1	G	31418	0.04
83	2	O	31418	0.04
84	1	G	31132	0.03
84	2	P	31132	0.03
85	1	H	31936	0.03
85	2	I	31936	0.03
86	1	H	31662	0.04
86	2	J	31662	0.04
87	1	H	31818	0.04
87	2	K	31818	0.04
88	1	H	31576	0.04
88	2	L	31576	0.04
89	1	H	31286	0.04
89	2	M	31286	0.04
90	1	H	31832	0.03
90	2	N	31832	0.03
91	1	H	31408	0.04
91	2	O	31408	0.04
92	1	H	31072	0.04
92	2	P	31072	0.04
93	1	I	31742	0.04
93	2	J	31742	0.04
94	1	I	31720	0.04
94	2	K	31720	0.04
95	1	I	31554	0.04
95	2	L	31554	0.04
96	1	I	31436	0.03
96	2	M	31436	0.03
97	1	I	31812	0.03
97	2	N	31812	0.03
98	1	I	31304	0.04
98	2	O	31304	0.04
99	1	I	30878	0.04
99	2	P	30878	0.04
100	1	J	31782	0.04
100	2	K	31782	0.04
101	1	J	31558	0.04
101	2	L	31558	0.04
102	1	J	31432	0.03
102	2	M	31432	0.03
103	1	J	31648	0.03
103	2	N	31648	0.03
104	1	J	31384	0.04
104	2	O	31384	0.04
105	1	J	31122	0.03
105	2	P	31122	0.03
106	1	K	31592	0.04
106	2	L	31592	0.04
107	1	K	31348	0.03
107	2	M	31348	0.03
108	1	K	31704	0.04
108	2	N	31704	0.04
109	1	K	31320	0.04
109	2	O	31320	0.04
110	1	K	31124	0.03
110	2	P	31124	0.03
111	1	L	31124	0.04
111	2	M	31124	0.04
112	1	L	31444	0.04
112	2	N	31444	0.04
113	1	L	31282	0.03
113	2	O	31282	0.03
114	1	L	30868	0.04
114	2	P	30868	0.04
115	1	M	31352	0.03
115	2	N	31352	0.03
116	1	M	31066	0.03
116	2	O	31066	0.03
117	1	M	30758	0.03
117	2	P	30758	0.03
118	1	N	31218	0.03
118	2	O	31218	0.03
119	1	N	30938	0.03
119	2	P	30938	0.03
120	1	O	31098	0.04
120	2	P	31098	0.04

LS refinement shell

Resolution: 3.19→3.273 Å / R_factor R_free error: 0 /

	R_factor	Num. reflection
R_free	0.432	13
R_work	0.335	146

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	0.1966	-0.0265	-0.096	0.1712	0.1534	0.357	-0.0487	-0.0117	0.0584	0.0705	0.0735	-0.0415	0.1361	0.0507	-0.0247	0.1275	0.0112	-0.0706	0.1325	0.0215	0.2887	85.9745	39.7079	-58.0129
2	0.0684	-0.0681	-0.0896	0.1903	-0.0232	0.3898	0.0723	-0.035	-0.0018	-0.0876	0.0723	-0.0563	-0.1247	0.05	-0.1446	0.1455	-0.0213	0.0791	0.1326	-0.0024	0.3036	89.6764	70.4494	-75.443
3	0.0585	-0.0365	-0.087	0.2296	0.1406	0.2924	0.0947	0.0148	-0.0141	0.006	-0.0145	-0.0497	-0.131	-0.1205	-0.0802	0.2044	0.0582	0.0133	0.17	0.0056	0.2023	52.4725	75.5577	-64.3109
4	0.0781	-0.0378	-0.1163	0.2352	0.0831	0.4625	0.006	0.0379	0.0045	-0.0136	-0.0985	-0.0109	0.0431	-0.111	0.0925	0.0972	-0.0308	-0.0341	0.2032	-0.022	0.2337	49.8693	41.119	-73.528
5	0.0702	0.0099	-0.1264	0.3132	0.0603	0.2824	-0.0348	0.007	0.0201	0.0162	0.0305	-0.0897	0.1311	0.0111	0.0043	0.2385	-0.0069	-0.0197	0.0634	0.0376	0.2708	45.9747	11.9546	0.6563
6	0.256	-0.14	-0.0899	0.1291	0.0563	0.2673	-0.0549	0.0336	-0.0715	0.1311	-0.0575	0.113	0.0833	0.0397	0.1124	0.2938	-0.116	0.0959	0.0752	0.004	0.2316	12.0472	6.5269	9.1999
7	0.1296	0.1047	0.2043	0.2055	0.2452	0.3952	-0.0066	0.0123	0.0279	-0.0652	-0.0998	0.0574	-0.0013	-0.0739	0.1065	0.1948	-0.0022	-0.0125	0.1226	-0.061	0.265	6.5379	37.3714	-14.7599
8	0.1761	0.1327	-0.108	0.24	0.0809	0.2864	0.0817	-0.027	0.0211	0.0006	-0.0162	-0.0128	-0.053	-0.0057	-0.0655	0.2258	-0.0325	0.0074	0.1071	0.003	0.2161	35.2146	49.8014	2.1748
9	0.0387	-0.044	-0.0034	0.2853	-0.0384	0.3613	0.0801	-0.0256	-0.0704	0.0598	-0.0228	0.0603	-0.2	0.1712	-0.0573	0.337	-0.1612	-0.1153	0.1009	0.0195	0.1615	94.7254	28.5176	-125.9519
10	0.041	-0.0172	-0.1023	0.3659	0.0624	0.4349	0.0072	-0.0291	-0.0236	-0.028	0.0076	0.05	-0.0517	0.0044	-0.0148	0.263	-0.0352	-0.0468	0.0634	0.0139	0.2193	62.5813	17.8508	-136.5317
11	0.0794	0.1458	-0.0579	0.2923	-0.1008	0.1991	-0.0042	-0.0116	-0.0228	0.0675	-0.0269	-0.0578	0.1598	-0.0202	0.0311	0.352	-0.0421	-0.0661	0.0094	0.0221	0.2066	78.7454	-17.5825	-133.2222
12	0.1105	0.0245	0.1289	0.1376	-0.1494	0.4308	-0.0364	0.095	-0.0983	-0.0618	-0.0016	-0.073	-0.0272	0.1631	0.038	0.125	-0.024	-0.0352	0.1495	0.0151	0.3187	106.3959	-1.3258	-148.1979
13	0.1483	-0.0414	-0.1979	0.578	-0.199	0.4799	0.1365	-0.1449	0.0642	-0.0053	0.0529	0.0627	-0.1238	0.2426	-0.1894	0.2364	-0.0303	0.068	0.2375	-0.0419	0.1321	33.5566	-12.6031	-58.4145
14	0.2059	0.0814	0.0269	0.1301	0.0541	0.4299	0.1615	0.1533	0.007	0.0862	0.039	-0.0584	-0.1048	-0.1849	-0.2006	0.2658	0.1852	0.0852	0.2187	0.1105	0.1322	-0.0934	-16.1936	-67.889
15	0.1792	0.041	-0.1871	0.0571	0.0103	0.6604	-0.1753	-0.0257	0.0068	0.0312	-0.0167	0.0447	0.2298	0.0022	0.192	0.3395	0.0783	0.1103	0.0943	0.0468	0.1627	8.2546	-54.3459	-63.5652
16	0.0538	-0.0468	-0.1531	0.0855	0.1278	0.462	-0.02	-0.025	-0.0146	-0.0636	-0.0128	-0.0031	0.0697	0.1498	0.0328	0.2574	0.1613	0.1336	0.2972	0.0586	0.1123	37.7161	-44.6167	-80.5184

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	114 - 803
2	X-RAY DIFFRACTION	2	B	114 - 901
3	X-RAY DIFFRACTION	3	C	115 - 901
4	X-RAY DIFFRACTION	4	D	114 - 901
5	X-RAY DIFFRACTION	5	E	114 - 901
6	X-RAY DIFFRACTION	6	F	114 - 901
7	X-RAY DIFFRACTION	7	G	114 - 803
8	X-RAY DIFFRACTION	8	H	114 - 901
9	X-RAY DIFFRACTION	9	I	115 - 901
10	X-RAY DIFFRACTION	10	J	115 - 901
11	X-RAY DIFFRACTION	11	K	115 - 901
12	X-RAY DIFFRACTION	12	L	115 - 803
13	X-RAY DIFFRACTION	13	M	115 - 803
14	X-RAY DIFFRACTION	14	N	115 - 901
15	X-RAY DIFFRACTION	15	O	114 - 901
16	X-RAY DIFFRACTION	16	P	114 - 803

-
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://pdbjlvh1.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, 16 molecules ABCDEFGHIJKLMNOP

-
Non-polymers , 6 types, 107 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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, 16 molecules ABCDEFGHIJKLMNOP

-Non-polymers , 6 types, 107 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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, 16 molecules ABCDEFGHIJKLMNOP

-
Non-polymers , 6 types, 107 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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