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- PDB-7zx1: Crystal structure of Pol theta polymerase domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7zx1
TitleCrystal structure of Pol theta polymerase domain in complex with compound 22
Components
  • DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
  • DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
  • DNA polymerase thetaPOLQ
KeywordsTRANSFERASE / DNA polymerase / protein-DNA complex / DNA repair / inhibitor
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / error-prone translesion synthesis ...single-stranded DNA endodeoxyribonuclease activity / double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / error-prone translesion synthesis / DNA helicase activity / base-excision repair / protein homooligomerization / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / Golgi apparatus / magnesium ion binding / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA polymerase theta-like, helix-turn-helix domain / : / Helix-turn-helix domain / DNA_pol_Q helicase like region helical domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain ...DNA polymerase theta-like, helix-turn-helix domain / : / Helix-turn-helix domain / DNA_pol_Q helicase like region helical domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / Chem-K8I / DNA / DNA (> 10) / DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.829 Å
AuthorsKrajewski, W.W. / Turnbull, A.P. / Willis, S. / Charles, M. / Stockley, M. / Heald, R.A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery, Characterization, and Structure-Based Optimization of Small-Molecule In Vitro and In Vivo Probes for Human DNA Polymerase Theta.
Authors: Stockley, M.L. / Ferdinand, A. / Benedetti, G. / Blencowe, P. / Boyd, S.M. / Calder, M. / Charles, M.D. / Edwardes, L.V. / Ekwuru, T. / Finch, H. / Galbiati, A. / Geo, L. / Grande, D. / ...Authors: Stockley, M.L. / Ferdinand, A. / Benedetti, G. / Blencowe, P. / Boyd, S.M. / Calder, M. / Charles, M.D. / Edwardes, L.V. / Ekwuru, T. / Finch, H. / Galbiati, A. / Geo, L. / Grande, D. / Grinkevich, V. / Holliday, N.D. / Krajewski, W.W. / MacDonald, E. / Majithiya, J.B. / McCarron, H. / McWhirter, C.L. / Patel, V. / Pedder, C. / Rajendra, E. / Ranzani, M. / Rigoreau, L.J.M. / Robinson, H.M.R. / Schaedler, T. / Sirina, J. / Smith, G.C.M. / Swarbrick, M.E. / Turnbull, A.P. / Willis, S. / Heald, R.A.
History
DepositionMay 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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
AAA: DNA polymerase theta
BBB: DNA polymerase theta
CCC: DNA polymerase theta
DDD: DNA polymerase theta
EEE: DNA polymerase theta
FFF: DNA polymerase theta
GGG: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
HHH: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
III: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
JJJ: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
KKK: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
LLL: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
MMM: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
NNN: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
OOO: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
PPP: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
QQQ: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
RRR: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)548,35134
Polymers543,58518
Non-polymers4,76716
Water181
1
AAA: DNA polymerase theta
GGG: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
HHH: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
hetero molecules


  • defined by author&software
  • 91.5 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)91,5316
Polymers90,5973
Non-polymers9343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-25 kcal/mol
Surface area29620 Å2
MethodPISA
2
BBB: DNA polymerase theta
III: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
JJJ: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
hetero molecules


  • defined by author&software
  • 91.5 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)91,5316
Polymers90,5973
Non-polymers9343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-26 kcal/mol
Surface area29610 Å2
MethodPISA
3
CCC: DNA polymerase theta
KKK: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
LLL: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
hetero molecules


  • defined by author&software
  • 91.5 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)91,5316
Polymers90,5973
Non-polymers9343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-25 kcal/mol
Surface area29490 Å2
MethodPISA
4
DDD: DNA polymerase theta
MMM: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
NNN: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
hetero molecules


  • defined by author&software
  • 91.5 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)91,5316
Polymers90,5973
Non-polymers9343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-25 kcal/mol
Surface area29440 Å2
MethodPISA
5
EEE: DNA polymerase theta
OOO: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
PPP: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
hetero molecules


  • defined by author&software
  • 91.1 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)91,1135
Polymers90,5973
Non-polymers5152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-24 kcal/mol
Surface area29860 Å2
MethodPISA
6
FFF: DNA polymerase theta
QQQ: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
RRR: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
hetero molecules


  • defined by author&software
  • 91.1 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)91,1135
Polymers90,5973
Non-polymers5152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-24 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.589, 172.292, 289.209
Angle α, β, γ (deg.)90.000, 91.217, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74AAA
84EEE
95AAA
105FFF
116BBB
126CCC
137BBB
147DDD
158BBB
168EEE
179BBB
189FFF
1910CCC
2010DDD
2111CCC
2211EEE
2312CCC
2412FFF
2513DDD
2613EEE
2714DDD
2814FFF
2915EEE
3015FFF
3116GGG
3216III
3317GGG
3417KKK
3518GGG
3618MMM
3719GGG
3819OOO
3920GGG
4020QQQ
4121HHH
4221JJJ
4322HHH
4422LLL
4523HHH
4623NNN
4724HHH
4824PPP
4925HHH
5025RRR
5126III
5226KKK
5327III
5427MMM
5528III
5628OOO
5729III
5829QQQ
5930JJJ
6030LLL
6131JJJ
6231NNN
6332JJJ
6432PPP
6533JJJ
6633RRR
6734KKK
6834MMM
6935KKK
7035OOO
7136KKK
7236QQQ
7337LLL
7437NNN
7538LLL
7638PPP
7739LLL
7839RRR
7940MMM
8040OOO
8141MMM
8241QQQ
8342NNN
8442PPP
8543NNN
8643RRR
8744OOO
8844QQQ
8945PPP
9045RRR

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERVALVALAAAA1824 - 25905 - 726
211SERSERVALVALBBBB1824 - 25905 - 726
322SERSERVALVALAAAA1824 - 25905 - 726
422SERSERVALVALCCCC1824 - 25905 - 726
533SERSERVALVALAAAA1824 - 25905 - 726
633SERSERVALVALDDDD1824 - 25905 - 726
744SERSERVALVALAAAA1824 - 25905 - 726
844SERSERVALVALEEEE1824 - 25905 - 726
955SERSERVALVALAAAA1824 - 25905 - 726
1055SERSERVALVALFFFF1824 - 25905 - 726
1166SERSERVALVALBBBB1824 - 25905 - 726
1266SERSERVALVALCCCC1824 - 25905 - 726
1377SERSERVALVALBBBB1824 - 25905 - 726
1477SERSERVALVALDDDD1824 - 25905 - 726
1588SERSERVALVALBBBB1824 - 25905 - 726
1688SERSERVALVALEEEE1824 - 25905 - 726
1799SERSERVALVALBBBB1824 - 25905 - 726
1899SERSERVALVALFFFF1824 - 25905 - 726
191010SERSERVALVALCCCC1824 - 25905 - 726
201010SERSERVALVALDDDD1824 - 25905 - 726
211111SERSERVALVALCCCC1824 - 25905 - 726
221111SERSERVALVALEEEE1824 - 25905 - 726
231212SERSERVALVALCCCC1824 - 25905 - 726
241212SERSERVALVALFFFF1824 - 25905 - 726
251313SERSERVALVALDDDD1824 - 25905 - 726
261313SERSERVALVALEEEE1824 - 25905 - 726
271414SERSERVALVALDDDD1824 - 25905 - 726
281414SERSERVALVALFFFF1824 - 25905 - 726
291515SERSERVALVALEEEE1824 - 25905 - 726
301515SERSERVALVALFFFF1824 - 25905 - 726
311616DTDTDCDCGGGG2 - 171 - 16
321616DTDTDCDCIIII2 - 171 - 16
331717DTDTDCDCGGGG2 - 171 - 16
341717DTDTDCDCKKKK2 - 171 - 16
351818DTDTDCDCGGGG2 - 171 - 16
361818DTDTDCDCMMMM2 - 171 - 16
371919DTDTDCDCGGGG2 - 171 - 16
381919DTDTDCDCOOOO2 - 171 - 16
392020DTDTDCDCGGGG2 - 171 - 16
402020DTDTDCDCQQQQ2 - 171 - 16
412121DGDGDDGDDGHHHH1 - 131 - 13
422121DGDGDDGDDGJJJJ1 - 131 - 13
432222DGDGDDGDDGHHHH1 - 131 - 13
442222DGDGDDGDDGLLLL1 - 131 - 13
452323DGDGDDGDDGHHHH1 - 131 - 13
462323DGDGDDGDDGNNNN1 - 131 - 13
472424DGDGDDGDDGHHHH1 - 131 - 13
482424DGDGDDGDDGPPPP1 - 131 - 13
492525DGDGDDGDDGHHHH1 - 131 - 13
502525DGDGDDGDDGRRRR1 - 131 - 13
512626DTDTDCDCIIII2 - 171 - 16
522626DTDTDCDCKKKK2 - 171 - 16
532727DTDTDCDCIIII2 - 171 - 16
542727DTDTDCDCMMMM2 - 171 - 16
552828DTDTDCDCIIII2 - 171 - 16
562828DTDTDCDCOOOO2 - 171 - 16
572929DTDTDCDCIIII2 - 171 - 16
582929DTDTDCDCQQQQ2 - 171 - 16
593030DGDGDDGDDGJJJJ1 - 131 - 13
603030DGDGDDGDDGLLLL1 - 131 - 13
613131DGDGDDGDDGJJJJ1 - 131 - 13
623131DGDGDDGDDGNNNN1 - 131 - 13
633232DGDGDDGDDGJJJJ1 - 131 - 13
643232DGDGDDGDDGPPPP1 - 131 - 13
653333DGDGDDGDDGJJJJ1 - 131 - 13
663333DGDGDDGDDGRRRR1 - 131 - 13
673434DTDTDCDCKKKK2 - 171 - 16
683434DTDTDCDCMMMM2 - 171 - 16
693535DTDTDCDCKKKK2 - 171 - 16
703535DTDTDCDCOOOO2 - 171 - 16
713636DTDTDCDCKKKK2 - 171 - 16
723636DTDTDCDCQQQQ2 - 171 - 16
733737DGDGDDGDDGLLLL1 - 131 - 13
743737DGDGDDGDDGNNNN1 - 131 - 13
753838DGDGDDGDDGLLLL1 - 131 - 13
763838DGDGDDGDDGPPPP1 - 131 - 13
773939DGDGDDGDDGLLLL1 - 131 - 13
783939DGDGDDGDDGRRRR1 - 131 - 13
794040DTDTDCDCMMMM2 - 171 - 16
804040DTDTDCDCOOOO2 - 171 - 16
814141DTDTDCDCMMMM2 - 171 - 16
824141DTDTDCDCQQQQ2 - 171 - 16
834242DGDGDDGDDGNNNN1 - 131 - 13
844242DGDGDDGDDGPPPP1 - 131 - 13
854343DGDGDDGDDGNNNN1 - 131 - 13
864343DGDGDDGDDGRRRR1 - 131 - 13
874444DTDTDCDCOOOO2 - 171 - 16
884444DTDTDCDCQQQQ2 - 171 - 16
894545DGDGDDGDDGPPPP1 - 131 - 13
904545DGDGDDGDDGRRRR1 - 131 - 13

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60
31Local NCS retraints between domains: 61 62
32Local NCS retraints between domains: 63 64
33Local NCS retraints between domains: 65 66
34Local NCS retraints between domains: 67 68
35Local NCS retraints between domains: 69 70
36Local NCS retraints between domains: 71 72
37Local NCS retraints between domains: 73 74
38Local NCS retraints between domains: 75 76
39Local NCS retraints between domains: 77 78
40Local NCS retraints between domains: 79 80
41Local NCS retraints between domains: 81 82
42Local NCS retraints between domains: 83 84
43Local NCS retraints between domains: 85 86
44Local NCS retraints between domains: 87 88
45Local NCS retraints between domains: 89 90

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Components

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Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

#1: Protein
DNA polymerase theta / POLQ / DNA polymerase eta


Mass: 81771.719 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLQ, POLH / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS / References: UniProt: O75417, DNA-directed DNA polymerase

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DNA chain , 2 types, 12 molecules GGGIIIKKKMMMOOOQQQHHHJJJLLLNNNPPPRRR

#2: DNA chain
DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')


Mass: 4843.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')


Mass: 3982.596 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 17 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-K8I / (2~{S},3~{R})-1-[3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]-~{N}-methyl-~{N}-(3-methylphenyl)-3-oxidanyl-pyrrolidine-2-carboxamide


Mass: 418.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H21F3N4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.829→110.77 Å / Num. obs: 135467 / % possible obs: 97.7 % / Redundancy: 3.4 % / CC1/2: 0.967 / Rrim(I) all: 0.057 / Net I/σ(I): 13.1
Reflection shellResolution: 2.829→2.93 Å / Num. unique obs: 9869 / CC1/2: 0.783 / Rrim(I) all: 0.532

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZUS

7zus


Resolution: 2.829→50.005 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.777 / SU ML: 0.334 / Cross valid method: FREE R-VALUE / ESU R Free: 0.382
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2602 6877 5.078 %
Rwork0.2281 128539 -
all0.23 --
obs-135416 97.497 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 93.617 Å2
Baniso -1Baniso -2Baniso -3
1-4.254 Å20 Å22.15 Å2
2---4.202 Å2-0 Å2
3----0.143 Å2
Refinement stepCycle: LAST / Resolution: 2.829→50.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29008 3528 306 1 32843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01333875
X-RAY DIFFRACTIONr_bond_other_d0.0010.01529706
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0310.0151949
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.65246682
X-RAY DIFFRACTIONr_angle_other_deg1.2471.57268213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29253773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9722.521405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.795154829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.38715159
X-RAY DIFFRACTIONr_chiral_restr0.0870.24725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0236017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027405
X-RAY DIFFRACTIONr_nbd_refined0.2020.26229
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.226417
X-RAY DIFFRACTIONr_nbtor_refined0.1730.215928
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.215862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2483
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.221
X-RAY DIFFRACTIONr_nbd_other0.2460.292
X-RAY DIFFRACTIONr_mcbond_it7.03510.01815188
X-RAY DIFFRACTIONr_mcbond_other7.03510.01715187
X-RAY DIFFRACTIONr_mcangle_it10.9515.01118929
X-RAY DIFFRACTIONr_mcangle_other10.9515.01218930
X-RAY DIFFRACTIONr_scbond_it6.9710.60618687
X-RAY DIFFRACTIONr_scbond_other6.96710.60718684
X-RAY DIFFRACTIONr_scangle_it11.02615.85827753
X-RAY DIFFRACTIONr_scangle_other11.02515.85927751
X-RAY DIFFRACTIONr_lrange_it16.523202.572388
X-RAY DIFFRACTIONr_lrange_other16.523202.49972389
X-RAY DIFFRACTIONr_ncsr_local_group_10.0320.0519948
X-RAY DIFFRACTIONr_ncsr_local_group_20.0290.0520264
X-RAY DIFFRACTIONr_ncsr_local_group_30.0420.0519898
X-RAY DIFFRACTIONr_ncsr_local_group_40.0360.0520051
X-RAY DIFFRACTIONr_ncsr_local_group_50.0340.0520061
X-RAY DIFFRACTIONr_ncsr_local_group_60.0320.0519907
X-RAY DIFFRACTIONr_ncsr_local_group_70.0410.0519701
X-RAY DIFFRACTIONr_ncsr_local_group_80.0340.0519969
X-RAY DIFFRACTIONr_ncsr_local_group_90.0330.0519868
X-RAY DIFFRACTIONr_ncsr_local_group_100.0410.0519893
X-RAY DIFFRACTIONr_ncsr_local_group_110.0350.0520033
X-RAY DIFFRACTIONr_ncsr_local_group_120.0330.0520050
X-RAY DIFFRACTIONr_ncsr_local_group_130.0370.0519828
X-RAY DIFFRACTIONr_ncsr_local_group_140.0390.0519930
X-RAY DIFFRACTIONr_ncsr_local_group_150.0350.0519967
X-RAY DIFFRACTIONr_ncsr_local_group_160.0130.051259
X-RAY DIFFRACTIONr_ncsr_local_group_170.0070.051268
X-RAY DIFFRACTIONr_ncsr_local_group_180.0090.051265
X-RAY DIFFRACTIONr_ncsr_local_group_190.0090.051264
X-RAY DIFFRACTIONr_ncsr_local_group_200.0080.051267
X-RAY DIFFRACTIONr_ncsr_local_group_210.0120.051144
X-RAY DIFFRACTIONr_ncsr_local_group_220.0070.051145
X-RAY DIFFRACTIONr_ncsr_local_group_230.0080.051145
X-RAY DIFFRACTIONr_ncsr_local_group_240.0090.051145
X-RAY DIFFRACTIONr_ncsr_local_group_250.0080.051145
X-RAY DIFFRACTIONr_ncsr_local_group_260.0130.051262
X-RAY DIFFRACTIONr_ncsr_local_group_270.0130.051263
X-RAY DIFFRACTIONr_ncsr_local_group_280.010.051265
X-RAY DIFFRACTIONr_ncsr_local_group_290.0110.051265
X-RAY DIFFRACTIONr_ncsr_local_group_300.0130.051141
X-RAY DIFFRACTIONr_ncsr_local_group_310.010.051144
X-RAY DIFFRACTIONr_ncsr_local_group_320.0090.051145
X-RAY DIFFRACTIONr_ncsr_local_group_330.0080.051144
X-RAY DIFFRACTIONr_ncsr_local_group_340.0080.051268
X-RAY DIFFRACTIONr_ncsr_local_group_350.0080.051267
X-RAY DIFFRACTIONr_ncsr_local_group_360.0070.051272
X-RAY DIFFRACTIONr_ncsr_local_group_370.0070.051145
X-RAY DIFFRACTIONr_ncsr_local_group_380.0090.051144
X-RAY DIFFRACTIONr_ncsr_local_group_390.0090.051145
X-RAY DIFFRACTIONr_ncsr_local_group_400.0080.051270
X-RAY DIFFRACTIONr_ncsr_local_group_410.0070.051272
X-RAY DIFFRACTIONr_ncsr_local_group_420.0070.051147
X-RAY DIFFRACTIONr_ncsr_local_group_430.0060.051147
X-RAY DIFFRACTIONr_ncsr_local_group_440.0060.051271
X-RAY DIFFRACTIONr_ncsr_local_group_450.0050.051148
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.032370.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.032370.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.029330.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.029330.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.041820.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.041820.05009
47AAAX-RAY DIFFRACTIONLocal ncs0.035670.05009
48EEEX-RAY DIFFRACTIONLocal ncs0.035670.05009
59AAAX-RAY DIFFRACTIONLocal ncs0.033870.05009
510FFFX-RAY DIFFRACTIONLocal ncs0.033870.05009
611BBBX-RAY DIFFRACTIONLocal ncs0.031550.05009
612CCCX-RAY DIFFRACTIONLocal ncs0.031550.05009
713BBBX-RAY DIFFRACTIONLocal ncs0.041440.05009
714DDDX-RAY DIFFRACTIONLocal ncs0.041440.05009
815BBBX-RAY DIFFRACTIONLocal ncs0.034310.05009
816EEEX-RAY DIFFRACTIONLocal ncs0.034310.05009
917BBBX-RAY DIFFRACTIONLocal ncs0.033050.05009
918FFFX-RAY DIFFRACTIONLocal ncs0.033050.05009
1019CCCX-RAY DIFFRACTIONLocal ncs0.04070.05009
1020DDDX-RAY DIFFRACTIONLocal ncs0.04070.05009
1121CCCX-RAY DIFFRACTIONLocal ncs0.034570.05009
1122EEEX-RAY DIFFRACTIONLocal ncs0.034570.05009
1223CCCX-RAY DIFFRACTIONLocal ncs0.032570.05009
1224FFFX-RAY DIFFRACTIONLocal ncs0.032570.05009
1325DDDX-RAY DIFFRACTIONLocal ncs0.037380.05009
1326EEEX-RAY DIFFRACTIONLocal ncs0.037380.05009
1427DDDX-RAY DIFFRACTIONLocal ncs0.039380.05009
1428FFFX-RAY DIFFRACTIONLocal ncs0.039380.05009
1529EEEX-RAY DIFFRACTIONLocal ncs0.034790.05009
1530FFFX-RAY DIFFRACTIONLocal ncs0.034790.05009
1631GGGX-RAY DIFFRACTIONLocal ncs0.013010.05011
1632IIIX-RAY DIFFRACTIONLocal ncs0.013010.05011
1733GGGX-RAY DIFFRACTIONLocal ncs0.007140.05011
1734KKKX-RAY DIFFRACTIONLocal ncs0.007140.05011
1835GGGX-RAY DIFFRACTIONLocal ncs0.009420.05011
1836MMMX-RAY DIFFRACTIONLocal ncs0.009420.05011
1937GGGX-RAY DIFFRACTIONLocal ncs0.008990.05011
1938OOOX-RAY DIFFRACTIONLocal ncs0.008990.05011
2039GGGX-RAY DIFFRACTIONLocal ncs0.007850.05011
2040QQQX-RAY DIFFRACTIONLocal ncs0.007850.05011
2141HHHX-RAY DIFFRACTIONLocal ncs0.011720.05011
2142JJJX-RAY DIFFRACTIONLocal ncs0.011720.05011
2243HHHX-RAY DIFFRACTIONLocal ncs0.007110.05011
2244LLLX-RAY DIFFRACTIONLocal ncs0.007110.05011
2345HHHX-RAY DIFFRACTIONLocal ncs0.007610.05011
2346NNNX-RAY DIFFRACTIONLocal ncs0.007610.05011
2447HHHX-RAY DIFFRACTIONLocal ncs0.009020.05011
2448PPPX-RAY DIFFRACTIONLocal ncs0.009020.05011
2549HHHX-RAY DIFFRACTIONLocal ncs0.007920.05011
2550RRRX-RAY DIFFRACTIONLocal ncs0.007920.05011
2651IIIX-RAY DIFFRACTIONLocal ncs0.012590.05011
2652KKKX-RAY DIFFRACTIONLocal ncs0.012590.05011
2753IIIX-RAY DIFFRACTIONLocal ncs0.012820.05011
2754MMMX-RAY DIFFRACTIONLocal ncs0.012820.05011
2855IIIX-RAY DIFFRACTIONLocal ncs0.009540.05011
2856OOOX-RAY DIFFRACTIONLocal ncs0.009540.05011
2957IIIX-RAY DIFFRACTIONLocal ncs0.010630.05011
2958QQQX-RAY DIFFRACTIONLocal ncs0.010630.05011
3059JJJX-RAY DIFFRACTIONLocal ncs0.013240.05011
3060LLLX-RAY DIFFRACTIONLocal ncs0.013240.05011
3161JJJX-RAY DIFFRACTIONLocal ncs0.010320.05011
3162NNNX-RAY DIFFRACTIONLocal ncs0.010320.05011
3263JJJX-RAY DIFFRACTIONLocal ncs0.008640.05011
3264PPPX-RAY DIFFRACTIONLocal ncs0.008640.05011
3365JJJX-RAY DIFFRACTIONLocal ncs0.008450.05011
3366RRRX-RAY DIFFRACTIONLocal ncs0.008450.05011
3467KKKX-RAY DIFFRACTIONLocal ncs0.008490.05011
3468MMMX-RAY DIFFRACTIONLocal ncs0.008490.05011
3569KKKX-RAY DIFFRACTIONLocal ncs0.007730.05011
3570OOOX-RAY DIFFRACTIONLocal ncs0.007730.05011
3671KKKX-RAY DIFFRACTIONLocal ncs0.006660.05012
3672QQQX-RAY DIFFRACTIONLocal ncs0.006660.05012
3773LLLX-RAY DIFFRACTIONLocal ncs0.006980.05011
3774NNNX-RAY DIFFRACTIONLocal ncs0.006980.05011
3875LLLX-RAY DIFFRACTIONLocal ncs0.009130.05011
3876PPPX-RAY DIFFRACTIONLocal ncs0.009130.05011
3977LLLX-RAY DIFFRACTIONLocal ncs0.0090.05011
3978RRRX-RAY DIFFRACTIONLocal ncs0.0090.05011
4079MMMX-RAY DIFFRACTIONLocal ncs0.008430.05012
4080OOOX-RAY DIFFRACTIONLocal ncs0.008430.05012
4181MMMX-RAY DIFFRACTIONLocal ncs0.007150.05012
4182QQQX-RAY DIFFRACTIONLocal ncs0.007150.05012
4283NNNX-RAY DIFFRACTIONLocal ncs0.006950.05011
4284PPPX-RAY DIFFRACTIONLocal ncs0.006950.05011
4385NNNX-RAY DIFFRACTIONLocal ncs0.00640.05011
4386RRRX-RAY DIFFRACTIONLocal ncs0.00640.05011
4487OOOX-RAY DIFFRACTIONLocal ncs0.005580.05012
4488QQQX-RAY DIFFRACTIONLocal ncs0.005580.05012
4589PPPX-RAY DIFFRACTIONLocal ncs0.005190.05011
4590RRRX-RAY DIFFRACTIONLocal ncs0.005190.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.829-2.9020.3714830.3592960.351100970.6210.65796.85050.328
2.902-2.9820.3355020.32593430.326100880.7610.75297.59120.299
2.982-3.0680.3214940.30488500.30595560.7990.8197.78150.276
3.068-3.1620.3154660.28987410.2994430.8350.84397.50080.258
3.162-3.2650.2964330.24984780.25191620.8860.8997.26040.222
3.265-3.3790.2794630.24981310.2588000.8790.89997.65910.227
3.379-3.5060.3134140.25679500.25985970.8630.8997.28970.237
3.506-3.6490.2874130.25374760.25581170.8820.89897.19110.234
3.649-3.810.2653850.24373000.24478890.9090.9197.41410.229
3.81-3.9950.2613890.22269630.22475690.9170.92497.1330.213
3.995-4.2090.2673460.21865900.22171440.9160.92597.08850.212
4.209-4.4630.2293250.19662690.19767650.9320.94397.47230.194
4.463-4.7680.2093460.18359160.18463640.9450.94898.39720.185
4.768-5.1460.2153170.18355270.18559500.9360.94798.21850.187
5.146-5.6310.242400.20251510.20455060.930.94597.91140.208
5.631-6.2860.272530.22646160.22949740.9160.92897.8890.231
6.286-7.2390.2491980.22341220.22544140.9220.93597.87040.233
7.239-8.820.1951680.18834950.18837540.9530.95397.57590.204
8.82-12.2840.211700.18726880.18829530.9440.95796.78290.209
12.284-50.0050.432720.31616370.32117220.8280.86599.24510.358

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