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- PDB-6qug: GHK tagged MBP-Nup98(1-29) -

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Basic information

Entry
Database: PDB / ID: 6qug
TitleGHK tagged MBP-Nup98(1-29)
ComponentsMaltodextrin-binding protein,Nucleoporin, putative
KeywordsTRANSPORT PROTEIN / MBP fusion Nup98
Function / homology
Function and homology information


structural constituent of nuclear pore / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / mRNA transport ...structural constituent of nuclear pore / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / mRNA transport / nuclear pore / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / protein transport / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Nuclear pore complex protein NUP98-NUP96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site ...Nuclear pore complex protein NUP98-NUP96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
COPPER (II) ION / PHOSPHATE ION / Maltodextrin-binding protein / Nucleoporin, putative / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Tetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsHuyton, T. / Gorlich, D.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography.
Authors: Mehr, A. / Henneberg, F. / Chari, A. / Gorlich, D. / Huyton, T.
History
DepositionFeb 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_symmetry / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 9, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / citation_author / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_ncs_dom_lim / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr_ncs.pdbx_number / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _reflns.d_resolution_low / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _software.version / _struct_ncs_dom_lim.end_auth_seq_id / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id
Description: Atomic clashes / Details: re-refined at reviewers request / Provider: author / Type: Coordinate replacement
Revision 3.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Nucleoporin, putative
B: Maltodextrin-binding protein,Nucleoporin, putative
C: Maltodextrin-binding protein,Nucleoporin, putative
D: Maltodextrin-binding protein,Nucleoporin, putative
E: Maltodextrin-binding protein,Nucleoporin, putative
F: Maltodextrin-binding protein,Nucleoporin, putative
G: Maltodextrin-binding protein,Nucleoporin, putative
H: Maltodextrin-binding protein,Nucleoporin, putative
I: Maltodextrin-binding protein,Nucleoporin, putative
J: Maltodextrin-binding protein,Nucleoporin, putative
K: Maltodextrin-binding protein,Nucleoporin, putative
L: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)525,74843
Polymers520,21012
Non-polymers5,53831
Water4,900272
1
A: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7573
Polymers43,3511
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7573
Polymers43,3511
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8534
Polymers43,3511
Non-polymers5023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9475
Polymers43,3511
Non-polymers5964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7573
Polymers43,3511
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7573
Polymers43,3511
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7573
Polymers43,3511
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7573
Polymers43,3511
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8524
Polymers43,3511
Non-polymers5013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8524
Polymers43,3511
Non-polymers5013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8534
Polymers43,3511
Non-polymers5023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Maltodextrin-binding protein,Nucleoporin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8534
Polymers43,3511
Non-polymers5023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.910, 286.780, 110.780
Angle α, β, γ (deg.)90.000, 92.010, 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
112B
212C
113B
213D
114B
214E
115B
215F
116B
216G
117B
217H
118B
218I
119B
219J
120B
220K
121B
221L
122C
222D
123C
223E
124C
224F
125C
225G
126C
226H
127C
227I
128C
228J
129C
229K
130C
230L
131D
231E
132D
232F
133D
233G
134D
234H
135D
235I
136D
236J
137D
237K
138D
238L
139E
239F
140E
240G
141E
241H
142E
242I
143E
243J
144E
244K
145E
245L
146F
246G
147F
247H
148F
248I
149F
249J
150F
250K
151F
251L
152G
252H
153G
253I
154G
254J
155G
255K
156G
256L
157H
257I
158H
258J
159H
259K
160H
260L
161I
261J
162I
262K
163I
263L
164J
264K
165J
265L
166K
266L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A-2 - 370
2010B-2 - 370
1020A-2 - 370
2020C-2 - 370
1030A-2 - 370
2030D-2 - 370
1040A-2 - 370
2040E-2 - 370
1050A-2 - 370
2050F-2 - 370
1060A-2 - 370
2060G-2 - 370
1070A-2 - 370
2070H-2 - 370
1080A-2 - 368
2080I-2 - 368
1090A-2 - 370
2090J-2 - 370
10100A-2 - 370
20100K-2 - 370
10110A-2 - 368
20110L-2 - 368
10120B-2 - 370
20120C-2 - 370
10130B-2 - 370
20130D-2 - 370
10140B-2 - 370
20140E-2 - 370
10150B-2 - 370
20150F-2 - 370
10160B-2 - 370
20160G-2 - 370
10170B-2 - 370
20170H-2 - 370
10180B-2 - 368
20180I-2 - 368
10190B-2 - 370
20190J-2 - 370
10200B-2 - 370
20200K-2 - 370
10210B-2 - 368
20210L-2 - 368
10220C-2 - 370
20220D-2 - 370
10230C-2 - 370
20230E-2 - 370
10240C-2 - 370
20240F-2 - 370
10250C-2 - 370
20250G-2 - 370
10260C-2 - 370
20260H-2 - 370
10270C-2 - 368
20270I-2 - 368
10280C-2 - 370
20280J-2 - 370
10290C-2 - 370
20290K-2 - 370
10300C-2 - 368
20300L-2 - 368
10310D-2 - 370
20310E-2 - 370
10320D-2 - 370
20320F-2 - 370
10330D-2 - 370
20330G-2 - 370
10340D-2 - 370
20340H-2 - 370
10350D-2 - 368
20350I-2 - 368
10360D-2 - 370
20360J-2 - 370
10370D-2 - 370
20370K-2 - 370
10380D-2 - 368
20380L-2 - 368
10390E-2 - 370
20390F-2 - 370
10400E-2 - 370
20400G-2 - 370
10410E-2 - 370
20410H-2 - 370
10420E-2 - 368
20420I-2 - 368
10430E-2 - 370
20430J-2 - 370
10440E-2 - 370
20440K-2 - 370
10450E-2 - 368
20450L-2 - 368
10460F-2 - 370
20460G-2 - 370
10470F-2 - 370
20470H-2 - 370
10480F-2 - 368
20480I-2 - 368
10490F-2 - 370
20490J-2 - 370
10500F-2 - 370
20500K-2 - 370
10510F-2 - 368
20510L-2 - 368
10520G-2 - 370
20520H-2 - 370
10530G-2 - 368
20530I-2 - 368
10540G-2 - 370
20540J-2 - 370
10550G-2 - 370
20550K-2 - 370
10560G-2 - 368
20560L-2 - 368
10570H-2 - 368
20570I-2 - 368
10580H-2 - 370
20580J-2 - 370
10590H-2 - 370
20590K-2 - 370
10600H-2 - 368
20600L-2 - 368
10610I-2 - 368
20610J-2 - 368
10620I-2 - 368
20620K-2 - 368
10630I-2 - 369
20630L-2 - 369
10640J-2 - 370
20640K-2 - 370
10650J-2 - 368
20650L-2 - 368
10660K-2 - 368
20660L-2 - 368

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
55
56
57
58
59
60
61
62
63
64
65
66

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Components

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Protein / Sugars , 2 types, 24 molecules ABCDEFGHIJKL

#1: Protein
Maltodextrin-binding protein,Nucleoporin, putative


Mass: 43350.859 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote)
Gene: malE, NCTC8450_00456, NCTC9775_03059, TTHERM_00071070 / Strain: SB210 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A376KDN7, UniProt: I7MHJ5, UniProt: P0AEX9*PLUS
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 291 molecules

#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

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Experimental details

-
Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.3776 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 2.7→49.19 Å / Num. obs: 141017 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.998 / Rpim(I) all: 0.048 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 14015 / CC1/2: 0.657 / Rpim(I) all: 0.4109

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / SU B: 26.475 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 7064 5 %RANDOM
Rwork0.2073 ---
obs0.2083 133953 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.68 Å2 / Biso mean: 61.653 Å2 / Biso min: 31.04 Å2
Baniso -1Baniso -2Baniso -3
1--4.56 Å2-0 Å2-2.63 Å2
2--3.89 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 2.7→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34298 0 323 272 34893
Biso mean--53.37 49.33 -
Num. residues----4474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01335501
X-RAY DIFFRACTIONr_bond_other_d0.0010.01732863
X-RAY DIFFRACTIONr_angle_refined_deg1.341.65148220
X-RAY DIFFRACTIONr_angle_other_deg1.2881.58776632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80454462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0625.1941548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.776155724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1741560
X-RAY DIFFRACTIONr_chiral_restr0.0630.24726
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0239490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026819
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A118110.08
12B118110.08
21A118580.08
22C118580.08
31A118920.07
32D118920.07
41A119230.07
42E119230.07
51A119510.07
52F119510.07
61A119450.06
62G119450.06
71A119420.07
72H119420.07
81A118040.07
82I118040.07
91A119430.07
92J119430.07
101A118780.07
102K118780.07
111A118880.07
112L118880.07
121B118420.08
122C118420.08
131B119080.07
132D119080.07
141B117890.09
142E117890.09
151B117980.08
152F117980.08
161B118400.08
162G118400.08
171B118490.08
172H118490.08
181B118610.08
182I118610.08
191B118730.08
192J118730.08
201B118350.08
202K118350.08
211B118250.08
212L118250.08
221C119040.07
222D119040.07
231C118150.08
232E118150.08
241C118540.07
242F118540.07
251C119450.07
252G119450.07
261C118590.07
262H118590.07
271C118520.07
272I118520.07
281C119190.07
282J119190.07
291C119050.07
292K119050.07
301C118300.08
302L118300.08
311D119070.07
312E119070.07
321D118570.07
322F118570.07
331D118830.07
332G118830.07
341D118830.07
342H118830.07
351D118020.08
352I118020.08
361D119800.07
362J119800.07
371D119410.06
372K119410.06
381D118670.06
382L118670.06
391E119480.07
392F119480.07
401E119510.07
402G119510.07
411E119550.07
412H119550.07
421E117440.08
422I117440.08
431E119040.07
432J119040.07
441E118780.07
442K118780.07
451E118200.07
452L118200.07
461F119880.06
462G119880.06
471F119150.07
472H119150.07
481F118400.07
482I118400.07
491F119100.07
492J119100.07
501F118630.07
502K118630.07
511F119030.06
512L119030.06
521G119780.07
522H119780.07
531G118840.07
532I118840.07
541G119530.07
542J119530.07
551G119400.07
552K119400.07
561G118930.07
562L118930.07
571H118010.07
572I118010.07
581H119840.07
582J119840.07
591H119190.07
592K119190.07
601H118300.07
602L118300.07
611I118780.06
612J118780.06
621I118590.07
622K118590.07
631I118580.07
632L118580.07
641J119300.07
642K119300.07
651J118340.07
652L118340.07
661K119140.06
662L119140.06
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 551 -
Rwork0.32 9920 -
all-10471 -
obs--99.91 %
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)
10.2029-0.103-0.08910.643-0.65640.94060.0230.0041-0.0373-0.044-0.02660.08380.03650.0310.00360.52250.00740.08740.0123-0.02030.12944.95138.46249.531
20.15060.47770.27492.26720.96421.24570.0231-0.011-0.11-0.38320.1825-0.4242-0.4028-0.2844-0.20560.73310.01450.08690.1762-0.01510.098941.69547.34424.534
30.6988-0.47740.51780.64950.08931.06590.02040.1358-0.2068-0.03990.13810.182-0.08080.3625-0.15850.3668-0.00950.12040.24250.02280.1341-11.875122.28674.165
40.81450.48161.00391.16270.59991.5817-0.2144-0.17590.148-0.4087-0.076-0.0227-0.1499-0.17080.29030.6270.02580.14210.0467-0.02780.10330.27184.15152.215
51.8696-0.1123-0.68270.41830.67691.5617-0.1373-0.0659-0.76080.0529-0.1315-0.0403-0.1087-0.20340.26880.35-0.00870.11020.04790.03420.5045-11.95792.362116.957
61.1583-0.30440.35750.3824-0.52530.74640.00670.0065-0.22340.02020.00640.05360.0018-0.0206-0.01320.5170.02470.06130.0132-0.03250.148635.037161.26143.332
70.5414-0.4955-0.40860.72850.67890.97610.0599-0.06480.0846-0.1892-0.0143-0.1598-0.1741-0.0324-0.04560.51190.03950.21510.03120.00510.1630.86157.68799.469
80.3752-0.04250.33250.6522-0.44520.9335-0.0743-0.13830.2151-0.0997-0.00140.03180.0506-0.0440.07570.35780.02390.10890.0658-0.09640.261746.332138.32116.958
90.85710.68390.17141.3815-0.17190.26720.1834-0.0052-0.02020.2201-0.03110.112-0.12-0.0078-0.15220.5202-0.06660.17520.03830.00020.116129.65251.99193.32
100.1845-0.3498-0.12761.22070.43980.7595-0.0644-0.01550.07080.15960.0788-0.00630.1430.1255-0.01440.46770.0140.1270.1129-0.06070.14664.05129.25532.157
110.6992-0.2846-0.01740.2655-0.32961.25450.08070.0168-0.1135-0.0472-0.04920.0059-0.10330.0996-0.03150.39640.01430.13020.0947-0.08070.192125.15111.7100.427
120.3034-0.0544-0.07140.5999-0.24671.26240.1147-0.06560.1228-0.0742-0.0238-0.06330.0830.1032-0.09090.4383-0.02530.20860.0299-0.0540.1781-15.9664.72767.278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 16
2X-RAY DIFFRACTION1A17 - 72
3X-RAY DIFFRACTION1A73 - 118
4X-RAY DIFFRACTION1A119 - 245
5X-RAY DIFFRACTION1A246 - 282
6X-RAY DIFFRACTION1A283 - 351
7X-RAY DIFFRACTION1A352 - 370
8X-RAY DIFFRACTION1A401
9X-RAY DIFFRACTION2B-2 - 16
10X-RAY DIFFRACTION2B17 - 72
11X-RAY DIFFRACTION2B73 - 118
12X-RAY DIFFRACTION2B119 - 245
13X-RAY DIFFRACTION2B246 - 282
14X-RAY DIFFRACTION2B283 - 351
15X-RAY DIFFRACTION2B352 - 370
16X-RAY DIFFRACTION2B401
17X-RAY DIFFRACTION3C-2 - 16
18X-RAY DIFFRACTION3C17 - 72
19X-RAY DIFFRACTION3C73 - 118
20X-RAY DIFFRACTION3C119 - 245
21X-RAY DIFFRACTION3C246 - 282
22X-RAY DIFFRACTION3C283 - 351
23X-RAY DIFFRACTION3C352 - 370
24X-RAY DIFFRACTION3C401
25X-RAY DIFFRACTION4D-2 - 16
26X-RAY DIFFRACTION4D17 - 72
27X-RAY DIFFRACTION4D73 - 118
28X-RAY DIFFRACTION4D119 - 245
29X-RAY DIFFRACTION4D246 - 282
30X-RAY DIFFRACTION4D283 - 351
31X-RAY DIFFRACTION4D352 - 370
32X-RAY DIFFRACTION4D401
33X-RAY DIFFRACTION5E-2 - 16
34X-RAY DIFFRACTION5E17 - 72
35X-RAY DIFFRACTION5E73 - 118
36X-RAY DIFFRACTION5E119 - 245
37X-RAY DIFFRACTION5E246 - 282
38X-RAY DIFFRACTION5E283 - 351
39X-RAY DIFFRACTION5E352 - 370
40X-RAY DIFFRACTION5E401
41X-RAY DIFFRACTION6F-2 - 16
42X-RAY DIFFRACTION6F17 - 72
43X-RAY DIFFRACTION6F73 - 118
44X-RAY DIFFRACTION6F119 - 245
45X-RAY DIFFRACTION6F246 - 282
46X-RAY DIFFRACTION6F283 - 351
47X-RAY DIFFRACTION6F352 - 370
48X-RAY DIFFRACTION6F401
49X-RAY DIFFRACTION7G-2 - 16
50X-RAY DIFFRACTION7G17 - 72
51X-RAY DIFFRACTION7G73 - 118
52X-RAY DIFFRACTION7G119 - 245
53X-RAY DIFFRACTION7G246 - 282
54X-RAY DIFFRACTION7G283 - 351
55X-RAY DIFFRACTION7G352 - 370
56X-RAY DIFFRACTION7G401
57X-RAY DIFFRACTION8H-2 - 16
58X-RAY DIFFRACTION8H17 - 72
59X-RAY DIFFRACTION8H73 - 118
60X-RAY DIFFRACTION8H119 - 245
61X-RAY DIFFRACTION8H246 - 282
62X-RAY DIFFRACTION8H283 - 351
63X-RAY DIFFRACTION8H352 - 370
64X-RAY DIFFRACTION8H401
65X-RAY DIFFRACTION9I-2 - 16
66X-RAY DIFFRACTION9I17 - 72
67X-RAY DIFFRACTION9I73 - 118
68X-RAY DIFFRACTION9I119 - 245
69X-RAY DIFFRACTION9I246 - 282
70X-RAY DIFFRACTION9I283 - 351
71X-RAY DIFFRACTION9I352 - 370
72X-RAY DIFFRACTION9I401
73X-RAY DIFFRACTION10J-2 - 16
74X-RAY DIFFRACTION10J17 - 72
75X-RAY DIFFRACTION10J73 - 118
76X-RAY DIFFRACTION10J119 - 245
77X-RAY DIFFRACTION10J246 - 282
78X-RAY DIFFRACTION10J283 - 351
79X-RAY DIFFRACTION10J352 - 370
80X-RAY DIFFRACTION10J401
81X-RAY DIFFRACTION11K-2 - 16
82X-RAY DIFFRACTION11K17 - 72
83X-RAY DIFFRACTION11K73 - 118
84X-RAY DIFFRACTION11K119 - 245
85X-RAY DIFFRACTION11K246 - 282
86X-RAY DIFFRACTION11K283 - 351
87X-RAY DIFFRACTION11K352 - 370
88X-RAY DIFFRACTION11K401
89X-RAY DIFFRACTION12L-2 - 16
90X-RAY DIFFRACTION12L17 - 72
91X-RAY DIFFRACTION12L73 - 118
92X-RAY DIFFRACTION12L119 - 245
93X-RAY DIFFRACTION12L246 - 282
94X-RAY DIFFRACTION12L283 - 351
95X-RAY DIFFRACTION12L352 - 370
96X-RAY DIFFRACTION12L401

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