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- PDB-6txa: Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6txa
TitleCrystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dGMPNPP and Mg
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / 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 ...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 / dGTP catabolic process / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Chem-CZF / : / Chem-XG4 / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.853 Å
AuthorsMorris, E.R. / Kunzelmann, S. / Caswell, S.J. / Arnold, L.H. / Purkiss, A. / Kelly, G. / Taylor, I.A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust108014/Z/15/Z United Kingdom
Wellcome TrustFC001178 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001178 United Kingdom
Cancer Research UKFC001178 United Kingdom
CitationJournal: 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
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: 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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)991,411143
Polymers963,32516
Non-polymers28,086127
Water00
1
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,87736
Polymers240,8314
Non-polymers7,04632
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,87736
Polymers240,8314
Non-polymers7,04632
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
J: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
K: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
L: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,87736
Polymers240,8314
Non-polymers7,04632
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
N: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
O: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
P: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,78135
Polymers240,8314
Non-polymers6,94931
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.782, 172.897, 275.886
Angle α, β, γ (deg.)90.000, 95.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116B
216C
117B
217D
118B
218E
119B
219F
120B
220G
121B
221H
122B
222I
123B
223J
124B
224K
125B
225L
126B
226M
127B
227N
128B
228O
129B
229P
130C
230D
131C
231E
132C
232F
133C
233G
134C
234H
135C
235I
136C
236J
137C
237K
138C
238L
139C
239M
140C
240N
141C
241O
142C
242P
143D
243E
144D
244F
145D
245G
146D
246H
147D
247I
148D
248J
149D
249K
150D
250L
151D
251M
152D
252N
153D
253O
154D
254P
155E
255F
156E
256G
157E
257H
158E
258I
159E
259J
160E
260K
161E
261L
162E
262M
163E
263N
164E
264O
165E
265P
166F
266G
167F
267H
168F
268I
169F
269J
170F
270K
171F
271L
172F
272M
173F
273N
174F
274O
175F
275P
176G
276H
177G
277I
178G
278J
179G
279K
180G
280L
181G
281M
182G
282N
183G
283O
184G
284P
185H
285I
186H
286J
187H
287K
188H
288L
189H
289M
190H
290N
191H
291O
192H
292P
193I
293J
194I
294K
195I
295L
196I
296M
197I
297N
198I
298O
199I
299P
1100J
2100K
1101J
2101L
1102J
2102M
1103J
2103N
1104J
2104O
1105J
2105P
1106K
2106L
1107K
2107M
1108K
2108N
1109K
2109O
1110K
2110P
1111L
2111M
1112L
2112N
1113L
2113O
1114L
2114P
1115M
2115N
1116M
2116O
1117M
2117P
1118N
2118O
1119N
2119P
1120O
2120P

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASNASNAA114 - 5998 - 493
21THRTHRASNASNBB114 - 5998 - 493
12METMETASNASNAA115 - 5999 - 493
22METMETASNASNCC115 - 5999 - 493
13THRTHRASNASNAA114 - 5998 - 493
23THRTHRASNASNDD114 - 5998 - 493
14THRTHRASNASNAA114 - 5998 - 493
24THRTHRASNASNEE114 - 5998 - 493
15THRTHRTRPTRPAA114 - 5988 - 492
25THRTHRTRPTRPFF114 - 5988 - 492
16THRTHRGLUGLUAA114 - 5978 - 491
26THRTHRGLUGLUGG114 - 5978 - 491
17THRTHRASNASNAA114 - 5998 - 493
27THRTHRASNASNHH114 - 5998 - 493
18METMETTRPTRPAA115 - 5989 - 492
28METMETTRPTRPII115 - 5989 - 492
19METMETGLUGLUAA115 - 5979 - 491
29METMETGLUGLUJJ115 - 5979 - 491
110METMETASNASNAA115 - 5999 - 493
210METMETASNASNKK115 - 5999 - 493
111METMETASNASNAA115 - 5999 - 493
211METMETASNASNLL115 - 5999 - 493
112METMETASNASNAA115 - 5999 - 493
212METMETASNASNMM115 - 5999 - 493
113METMETASNASNAA115 - 5999 - 493
213METMETASNASNNN115 - 5999 - 493
114THRTHRASNASNAA114 - 5998 - 493
214THRTHRASNASNOO114 - 5998 - 493
115THRTHRTRPTRPAA114 - 5988 - 492
215THRTHRTRPTRPPP114 - 5988 - 492
116METMETASNASNBB115 - 5999 - 493
216METMETASNASNCC115 - 5999 - 493
117THRTHRASNASNBB114 - 5998 - 493
217THRTHRASNASNDD114 - 5998 - 493
118THRTHRASNASNBB114 - 5998 - 493
218THRTHRASNASNEE114 - 5998 - 493
119THRTHRGLUGLUBB114 - 5978 - 491
219THRTHRGLUGLUFF114 - 5978 - 491
120THRTHRTRPTRPBB114 - 5988 - 492
220THRTHRTRPTRPGG114 - 5988 - 492
121THRTHRASNASNBB114 - 5998 - 493
221THRTHRASNASNHH114 - 5998 - 493
122METMETASNASNBB115 - 5999 - 493
222METMETASNASNII115 - 5999 - 493
123METMETGLUGLUBB115 - 5979 - 491
223METMETGLUGLUJJ115 - 5979 - 491
124METMETTRPTRPBB115 - 5989 - 492
224METMETTRPTRPKK115 - 5989 - 492
125METMETTRPTRPBB115 - 5989 - 492
225METMETTRPTRPLL115 - 5989 - 492
126METMETASNASNBB115 - 5999 - 493
226METMETASNASNMM115 - 5999 - 493
127METMETASNASNBB115 - 5999 - 493
227METMETASNASNNN115 - 5999 - 493
128THRTHRASNASNBB114 - 5998 - 493
228THRTHRASNASNOO114 - 5998 - 493
129THRTHRGLUGLUBB114 - 5978 - 491
229THRTHRGLUGLUPP114 - 5978 - 491
130METMETTRPTRPCC115 - 5989 - 492
230METMETTRPTRPDD115 - 5989 - 492
131METMETASNASNCC115 - 5999 - 493
231METMETASNASNEE115 - 5999 - 493
132METMETTRPTRPCC115 - 5989 - 492
232METMETTRPTRPFF115 - 5989 - 492
133METMETGLUGLUCC115 - 5979 - 491
233METMETGLUGLUGG115 - 5979 - 491
134METMETASNASNCC115 - 5999 - 493
234METMETASNASNHH115 - 5999 - 493
135METMETASNASNCC115 - 5999 - 493
235METMETASNASNII115 - 5999 - 493
136METMETTRPTRPCC115 - 5989 - 492
236METMETTRPTRPJJ115 - 5989 - 492
137METMETASNASNCC115 - 5999 - 493
237METMETASNASNKK115 - 5999 - 493
138METMETASNASNCC115 - 5999 - 493
238METMETASNASNLL115 - 5999 - 493
139METMETASNASNCC115 - 5999 - 493
239METMETASNASNMM115 - 5999 - 493
140METMETASNASNCC115 - 5999 - 493
240METMETASNASNNN115 - 5999 - 493
141METMETASNASNCC115 - 5999 - 493
241METMETASNASNOO115 - 5999 - 493
142METMETTRPTRPCC115 - 5989 - 492
242METMETTRPTRPPP115 - 5989 - 492
143THRTHRASNASNDD114 - 5998 - 493
243THRTHRASNASNEE114 - 5998 - 493
144THRTHRTRPTRPDD114 - 5988 - 492
244THRTHRTRPTRPFF114 - 5988 - 492
145THRTHRTRPTRPDD114 - 5988 - 492
245THRTHRTRPTRPGG114 - 5988 - 492
146THRTHRASNASNDD114 - 5998 - 493
246THRTHRASNASNHH114 - 5998 - 493
147METMETASNASNDD115 - 5999 - 493
247METMETASNASNII115 - 5999 - 493
148METMETGLUGLUDD115 - 5979 - 491
248METMETGLUGLUJJ115 - 5979 - 491
149METMETASNASNDD115 - 5999 - 493
249METMETASNASNKK115 - 5999 - 493
150METMETASNASNDD115 - 5999 - 493
250METMETASNASNLL115 - 5999 - 493
151METMETASNASNDD115 - 5999 - 493
251METMETASNASNMM115 - 5999 - 493
152METMETASNASNDD115 - 5999 - 493
252METMETASNASNNN115 - 5999 - 493
153THRTHRASNASNDD114 - 5998 - 493
253THRTHRASNASNOO114 - 5998 - 493
154THRTHRTRPTRPDD114 - 5988 - 492
254THRTHRTRPTRPPP114 - 5988 - 492
155THRTHRGLUGLUEE114 - 5978 - 491
255THRTHRGLUGLUFF114 - 5978 - 491
156THRTHRTRPTRPEE114 - 5988 - 492
256THRTHRTRPTRPGG114 - 5988 - 492
157THRTHRASNASNEE114 - 5998 - 493
257THRTHRASNASNHH114 - 5998 - 493
158METMETASNASNEE115 - 5999 - 493
258METMETASNASNII115 - 5999 - 493
159METMETGLUGLUEE115 - 5979 - 491
259METMETGLUGLUJJ115 - 5979 - 491
160METMETTRPTRPEE115 - 5989 - 492
260METMETTRPTRPKK115 - 5989 - 492
161METMETTRPTRPEE115 - 5989 - 492
261METMETTRPTRPLL115 - 5989 - 492
162METMETASNASNEE115 - 5999 - 493
262METMETASNASNMM115 - 5999 - 493
163METMETASNASNEE115 - 5999 - 493
263METMETASNASNNN115 - 5999 - 493
164THRTHRASNASNEE114 - 5998 - 493
264THRTHRASNASNOO114 - 5998 - 493
165THRTHRGLUGLUEE114 - 5978 - 491
265THRTHRGLUGLUPP114 - 5978 - 491
166THRTHRTRPTRPFF114 - 5988 - 492
266THRTHRTRPTRPGG114 - 5988 - 492
167THRTHRTRPTRPFF114 - 5988 - 492
267THRTHRTRPTRPHH114 - 5988 - 492
168METMETGLUGLUFF115 - 5979 - 491
268METMETGLUGLUII115 - 5979 - 491
169METMETTRPTRPFF115 - 5989 - 492
269METMETTRPTRPJJ115 - 5989 - 492
170METMETGLUGLUFF115 - 5979 - 491
270METMETGLUGLUKK115 - 5979 - 491
171METMETGLUGLUFF115 - 5979 - 491
271METMETGLUGLULL115 - 5979 - 491
172METMETTRPTRPFF115 - 5989 - 492
272METMETTRPTRPMM115 - 5989 - 492
173METMETGLUGLUFF115 - 5979 - 491
273METMETGLUGLUNN115 - 5979 - 491
174THRTHRTRPTRPFF114 - 5988 - 492
274THRTHRTRPTRPOO114 - 5988 - 492
175THRTHRTRPTRPFF114 - 5988 - 492
275THRTHRTRPTRPPP114 - 5988 - 492
176THRTHRGLUGLUGG114 - 5978 - 491
276THRTHRGLUGLUHH114 - 5978 - 491
177METMETGLUGLUGG115 - 5979 - 491
277METMETGLUGLUII115 - 5979 - 491
178METMETGLUGLUGG115 - 5979 - 491
278METMETGLUGLUJJ115 - 5979 - 491
179METMETGLUGLUGG115 - 5979 - 491
279METMETGLUGLUKK115 - 5979 - 491
180METMETGLUGLUGG115 - 5979 - 491
280METMETGLUGLULL115 - 5979 - 491
181METMETTRPTRPGG115 - 5989 - 492
281METMETTRPTRPMM115 - 5989 - 492
182METMETTRPTRPGG115 - 5989 - 492
282METMETTRPTRPNN115 - 5989 - 492
183THRTHRTRPTRPGG114 - 5988 - 492
283THRTHRTRPTRPOO114 - 5988 - 492
184THRTHRTRPTRPGG114 - 5988 - 492
284THRTHRTRPTRPPP114 - 5988 - 492
185METMETTRPTRPHH115 - 5989 - 492
285METMETTRPTRPII115 - 5989 - 492
186METMETGLUGLUHH115 - 5979 - 491
286METMETGLUGLUJJ115 - 5979 - 491
187METMETASNASNHH115 - 5999 - 493
287METMETASNASNKK115 - 5999 - 493
188METMETASNASNHH115 - 5999 - 493
288METMETASNASNLL115 - 5999 - 493
189METMETASNASNHH115 - 5999 - 493
289METMETASNASNMM115 - 5999 - 493
190METMETASNASNHH115 - 5999 - 493
290METMETASNASNNN115 - 5999 - 493
191THRTHRASNASNHH114 - 5998 - 493
291THRTHRASNASNOO114 - 5998 - 493
192THRTHRTRPTRPHH114 - 5988 - 492
292THRTHRTRPTRPPP114 - 5988 - 492
193METMETGLUGLUII115 - 5979 - 491
293METMETGLUGLUJJ115 - 5979 - 491
194METMETASNASNII115 - 5999 - 493
294METMETASNASNKK115 - 5999 - 493
195METMETASNASNII115 - 5999 - 493
295METMETASNASNLL115 - 5999 - 493
196METMETASNASNII115 - 5999 - 493
296METMETASNASNMM115 - 5999 - 493
197METMETASNASNII115 - 5999 - 493
297METMETASNASNNN115 - 5999 - 493
198METMETASNASNII115 - 5999 - 493
298METMETASNASNOO115 - 5999 - 493
199METMETGLUGLUII115 - 5979 - 491
299METMETGLUGLUPP115 - 5979 - 491
1100METMETTRPTRPJJ115 - 5989 - 492
2100METMETTRPTRPKK115 - 5989 - 492
1101METMETTRPTRPJJ115 - 5989 - 492
2101METMETTRPTRPLL115 - 5989 - 492
1102METMETTRPTRPJJ115 - 5989 - 492
2102METMETTRPTRPMM115 - 5989 - 492
1103METMETTRPTRPJJ115 - 5989 - 492
2103METMETTRPTRPNN115 - 5989 - 492
1104METMETTRPTRPJJ115 - 5989 - 492
2104METMETTRPTRPOO115 - 5989 - 492
1105METMETTRPTRPJJ115 - 5989 - 492
2105METMETTRPTRPPP115 - 5989 - 492
1106METMETASNASNKK115 - 5999 - 493
2106METMETASNASNLL115 - 5999 - 493
1107METMETASNASNKK115 - 5999 - 493
2107METMETASNASNMM115 - 5999 - 493
1108METMETASNASNKK115 - 5999 - 493
2108METMETASNASNNN115 - 5999 - 493
1109METMETASNASNKK115 - 5999 - 493
2109METMETASNASNOO115 - 5999 - 493
1110METMETGLUGLUKK115 - 5979 - 491
2110METMETGLUGLUPP115 - 5979 - 491
1111METMETASNASNLL115 - 5999 - 493
2111METMETASNASNMM115 - 5999 - 493
1112METMETTRPTRPLL115 - 5989 - 492
2112METMETTRPTRPNN115 - 5989 - 492
1113METMETASNASNLL115 - 5999 - 493
2113METMETASNASNOO115 - 5999 - 493
1114METMETGLUGLULL115 - 5979 - 491
2114METMETGLUGLUPP115 - 5979 - 491
1115METMETASNASNMM115 - 5999 - 493
2115METMETASNASNNN115 - 5999 - 493
1116METMETASNASNMM115 - 5999 - 493
2116METMETASNASNOO115 - 5999 - 493
1117METMETTRPTRPMM115 - 5989 - 492
2117METMETTRPTRPPP115 - 5989 - 492
1118METMETASNASNNN115 - 5999 - 493
2118METMETASNASNOO115 - 5999 - 493
1119METMETGLUGLUNN115 - 5979 - 491
2119METMETGLUGLUPP115 - 5979 - 491
1120THRTHRTRPTRPOO114 - 5988 - 492
2120THRTHRTRPTRPPP114 - 5988 - 492

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
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111
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113
114
115
116
117
118
119
120

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Components

-
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: 60207.816 Da / Num. of mol.: 16 / Mutation: D137N
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 , 5 types, 127 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.: 48 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine


Mass: 506.196 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CZF / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate / xanthosine triphosphate


Mass: 524.165 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N4O15P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.85→146.334 Å / Num. obs: 140978 / % possible obs: 94.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 49.5 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.117 / Rrim(I) all: 0.22 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.853-3.2013.40.5771.570490.7290.3640.68467.3
8.918-146.3343.30.04910.470470.9960.0310.05899.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation9.57 Å274.75 Å
Translation9.57 Å274.75 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.7.4data scaling
STARANISOdata scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TX0

6tx0


Resolution: 2.853→146.243 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.893 / SU B: 49.724 / SU ML: 0.384 / SU R Cruickshank DPI: 0.4486 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.483
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 7029 5 %RANDOM
Rwork0.1944 ---
obs0.1953 133948 66.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 175.01 Å2 / Biso mean: 54.995 Å2 / Biso min: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å2-0.46 Å2
2---0.53 Å2-0 Å2
3---0.84 Å2
Refinement stepCycle: final / Resolution: 2.853→146.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61333 0 1643 0 62976
Biso mean--34.38 --
Num. residues----7666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01964483
X-RAY DIFFRACTIONr_bond_other_d0.0020.0257620
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.95187789
X-RAY DIFFRACTIONr_angle_other_deg1.0342.989133487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14357635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77623.9773118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6561510532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.91315403
X-RAY DIFFRACTIONr_chiral_restr0.0850.29495
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02171105
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0213246
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A320260.04
12B320260.04
21A318820.05
22C318820.05
31A318820.05
32D318820.05
41A319620.05
42E319620.05
51A318580.04
52F318580.04
61A316880.04
62G316880.04
71A319800.05
72H319800.05
81A317560.05
82I317560.05
91A316900.04
92J316900.04
101A319200.04
102K319200.04
111A314800.05
112L314800.05
121A315340.04
122M315340.04
131A317740.04
132N317740.04
141A317320.04
142O317320.04
151A317780.04
152P317780.04
161B318580.04
162C318580.04
171B318580.05
172D318580.05
181B320380.04
182E320380.04
191B315860.04
192F315860.04
201B317960.04
202G317960.04
211B319820.04
212H319820.04
221B318740.03
222I318740.03
231B316660.04
232J316660.04
241B317220.05
242K317220.05
251B314860.04
252L314860.04
261B315600.04
262M315600.04
271B317720.04
272N317720.04
281B318180.04
282O318180.04
291B315140.04
292P315140.04
301C317840.04
302D317840.04
311C319580.03
312E319580.03
321C316860.04
322F316860.04
331C316020.04
332G316020.04
341C320320.03
342H320320.03
351C319700.04
352I319700.04
361C317960.04
362J317960.04
371C319120.04
372K319120.04
381C315840.04
382L315840.04
391C316300.04
392M316300.04
401C318020.03
402N318020.03
411C317140.04
412O317140.04
421C316200.04
422P316200.04
431D319320.04
432E319320.04
441D317140.04
442F317140.04
451D318500.03
452G318500.03
461D319400.05
462H319400.05
471D318640.04
472I318640.04
481D318260.03
482J318260.03
491D317820.04
492K317820.04
501D316320.04
502L316320.04
511D317660.03
512M317660.03
521D316880.04
522N316880.04
531D318160.05
532O318160.05
541D316200.04
542P316200.04
551E316240.04
552F316240.04
561E317740.04
562G317740.04
571E320420.04
572H320420.04
581E319160.04
582I319160.04
591E318040.04
592J318040.04
601E318520.04
602K318520.04
611E316420.03
612L316420.03
621E316620.04
622M316620.04
631E318760.04
632N318760.04
641E318860.03
642O318860.03
651E315660.03
652P315660.03
661F318260.04
662G318260.04
671F317060.05
672H317060.05
681F314600.05
682I314600.05
691F316960.04
692J316960.04
701F316940.03
702K316940.03
711F314020.04
712L314020.04
721F315780.04
722M315780.04
731F314600.04
732N314600.04
741F318020.03
742O318020.03
751F317480.03
752P317480.03
761G316480.04
762H316480.04
771G316300.04
772I316300.04
781G316680.03
782J316680.03
791G314880.04
792K314880.04
801G313260.04
802L313260.04
811G316320.03
812M316320.03
821G316240.04
822N316240.04
831G317140.04
832O317140.04
841G316900.03
842P316900.03
851H319480.03
852I319480.03
861H317360.04
862J317360.04
871H318640.05
872K318640.05
881H315560.04
882L315560.04
891H316460.05
892M316460.05
901H319200.04
902N319200.04
911H317660.05
912O317660.05
921H316500.05
922P316500.05
931I316980.04
932J316980.04
941I317260.04
942K317260.04
951I316900.04
952L316900.04
961I317340.04
962M317340.04
971I318460.03
972N318460.03
981I318040.04
982O318040.04
991I314100.04
992P314100.04
1001J317840.04
1002K317840.04
1011J316000.04
1012L316000.04
1021J317000.03
1022M317000.03
1031J317300.03
1032N317300.03
1041J316920.04
1042O316920.04
1051J317020.03
1052P317020.03
1061K315520.04
1062L315520.04
1071K316820.03
1072M316820.03
1081K317840.04
1082N317840.04
1091K316840.05
1092O316840.05
1101K315120.04
1102P315120.04
1111L315740.04
1112M315740.04
1121L315820.04
1122N315820.04
1131L316640.03
1132O316640.03
1141L313340.04
1142P313340.04
1151M316740.03
1152N316740.03
1161M315920.03
1162O315920.03
1171M314740.04
1172P314740.04
1181N317020.03
1182O317020.03
1191N314180.04
1192P314180.04
1201O316240.04
1202P316240.04
LS refinement shellResolution: 2.853→2.927 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 31 -
Rwork0.351 671 -
all-702 -
obs--4.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.1725-0.0616-0.00910.07850.11680.3628-0.0024-0.00520.05350.03650.0651-0.03960.09140.0289-0.06270.04320.0070.00940.20140.01060.118785.922439.6669-58.193
20.1624-0.0912-0.04180.06660.08340.45630.1053-0.00050.068-0.07810.0052-0.0801-0.06370.0143-0.11050.10070.010.11450.14440.03330.177689.692670.4638-75.6608
30.0891-0.0444-0.1340.08670.13540.49750.07870.01340.0005-0.0383-0.0527-0.0546-0.1255-0.1766-0.02610.11120.07240.03040.23520.02780.087452.348775.6334-64.448
40.1234-0.0155-0.03680.08920.05910.33230.0390.0888-0.03570.004-0.1421-0.01330.0093-0.13670.10310.0353-0.00510.02290.2799-0.03360.092949.789141.1923-73.7639
50.1197-0.0794-0.16720.2390.0990.2533-0.0881-0.0337-0.0294-0.02730.0086-0.06830.12390.06750.07950.15010.03110.08730.10860.06010.131346.089211.92330.412
60.1794-0.0685-0.22130.03950.09470.4264-0.13380.0231-0.07950.0837-0.02340.05930.1243-0.01320.15720.2099-0.05350.120.08210.00940.138712.16236.52159.1603
70.09160.109-0.06870.31820.13120.37850.00060.01610.0004-0.0649-0.08480.0359-0.0203-0.09570.08420.1123-0.00220.00080.1844-0.0370.08436.555437.3704-14.701
80.1045-0.027-0.15040.15290.15410.34520.053-0.05260.0138-0.0304-0.0008-0.0217-0.05790.0126-0.05220.1187-0.02280.03470.15530.00820.101735.35549.84422.1108
90.0763-0.0355-0.05020.1876-0.05390.60240.0948-0.0427-0.04610.1178-0.10750.0126-0.26790.15860.01270.3028-0.1916-0.060.1290.02940.029294.641728.352-126.3019
100.0330.0922-0.03770.3165-0.03450.61590.0270.00140.0030.0325-0.01820.0528-0.0936-0.0876-0.00880.22-0.01970.02360.096-0.00780.059462.422717.7892-137.004
110.17060.2125-0.00270.2749-0.04820.40060.0427-0.0875-0.10620.0503-0.096-0.13180.1803-0.0710.05330.2846-0.0544-0.01460.06390.05450.088178.4968-17.792-133.7599
120.15160.05890.21580.2446-0.12810.68190.00110.0755-0.0989-0.065-0.0421-0.11040.01090.20330.0410.07440.03170.02850.14790.03630.2038106.1858-1.4875-148.819
130.12060.0062-0.24420.3469-0.10490.62270.1177-0.12930.080.00230.04540.0646-0.16810.2819-0.16310.1625-0.06770.0960.2346-0.04360.076433.5272-12.7658-58.6141
140.19930.0423-0.19230.14320.02380.49950.15940.12560.07690.0302-0.0059-0.0234-0.1112-0.174-0.15340.1590.14960.07480.20990.11350.0734-0.3249-16.312-68.2062
150.12790.0403-0.25010.03-0.12420.7521-0.1421-0.0195-0.0426-0.019-0.0048-0.01080.2486-0.06510.14690.23080.0510.10270.13620.00720.08187.6372-54.3317-63.9429
160.1484-0.0563-0.30070.03640.11050.6268-0.0608-0.0823-0.0272-0.03080.0007-0.01720.13650.22480.06010.20910.15150.10740.25310.0710.055537.7138-44.7796-80.5252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 901
2X-RAY DIFFRACTION2B114 - 901
3X-RAY DIFFRACTION3C115 - 901
4X-RAY DIFFRACTION4D114 - 901
5X-RAY DIFFRACTION5E114 - 901
6X-RAY DIFFRACTION6F114 - 901
7X-RAY DIFFRACTION7G114 - 901
8X-RAY DIFFRACTION8H114 - 901
9X-RAY DIFFRACTION9I115 - 901
10X-RAY DIFFRACTION10J115 - 901
11X-RAY DIFFRACTION11K115 - 901
12X-RAY DIFFRACTION12L115 - 901
13X-RAY DIFFRACTION13M115 - 901
14X-RAY DIFFRACTION14N115 - 901
15X-RAY DIFFRACTION15O114 - 901
16X-RAY DIFFRACTION16P114 - 803

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