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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


telomere tethering at nuclear periphery / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / nuclear localization sequence binding / RNA export from nucleus / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity ...telomere tethering at nuclear periphery / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / nuclear localization sequence binding / RNA export from nucleus / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / mRNA transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / protein import into nucleus / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / RNA binding / membrane
Similarity search - Function
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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / 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
Revision 3.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 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:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-2 - 3701 - 373
21BB-2 - 3701 - 373
12AA-2 - 3701 - 373
22CC-2 - 3701 - 373
13AA-2 - 3701 - 373
23DD-2 - 3701 - 373
14AA-2 - 3701 - 373
24EE-2 - 3701 - 373
15AA-2 - 3701 - 373
25FF-2 - 3701 - 373
16AA-2 - 3701 - 373
26GG-2 - 3701 - 373
17AA-2 - 3701 - 373
27HH-2 - 3701 - 373
18AA-2 - 3681 - 371
28II-2 - 3681 - 371
19AA-2 - 3701 - 373
29JJ-2 - 3701 - 373
110AA-2 - 3701 - 373
210KK-2 - 3701 - 373
111AA-2 - 3681 - 371
211LL-2 - 3681 - 371
112BB-2 - 3701 - 373
212CC-2 - 3701 - 373
113BB-2 - 3701 - 373
213DD-2 - 3701 - 373
114BB-2 - 3701 - 373
214EE-2 - 3701 - 373
115BB-2 - 3701 - 373
215FF-2 - 3701 - 373
116BB-2 - 3701 - 373
216GG-2 - 3701 - 373
117BB-2 - 3701 - 373
217HH-2 - 3701 - 373
118BB-2 - 3681 - 371
218II-2 - 3681 - 371
119BB-2 - 3701 - 373
219JJ-2 - 3701 - 373
120BB-2 - 3701 - 373
220KK-2 - 3701 - 373
121BB-2 - 3681 - 371
221LL-2 - 3681 - 371
122CC-2 - 3701 - 373
222DD-2 - 3701 - 373
123CC-2 - 3701 - 373
223EE-2 - 3701 - 373
124CC-2 - 3701 - 373
224FF-2 - 3701 - 373
125CC-2 - 3701 - 373
225GG-2 - 3701 - 373
126CC-2 - 3701 - 373
226HH-2 - 3701 - 373
127CC-2 - 3681 - 371
227II-2 - 3681 - 371
128CC-2 - 3701 - 373
228JJ-2 - 3701 - 373
129CC-2 - 3701 - 373
229KK-2 - 3701 - 373
130CC-2 - 3681 - 371
230LL-2 - 3681 - 371
131DD-2 - 3701 - 373
231EE-2 - 3701 - 373
132DD-2 - 3701 - 373
232FF-2 - 3701 - 373
133DD-2 - 3701 - 373
233GG-2 - 3701 - 373
134DD-2 - 3701 - 373
234HH-2 - 3701 - 373
135DD-2 - 3681 - 371
235II-2 - 3681 - 371
136DD-2 - 3701 - 373
236JJ-2 - 3701 - 373
137DD-2 - 3701 - 373
237KK-2 - 3701 - 373
138DD-2 - 3681 - 371
238LL-2 - 3681 - 371
139EE-2 - 3701 - 373
239FF-2 - 3701 - 373
140EE-2 - 3701 - 373
240GG-2 - 3701 - 373
141EE-2 - 3701 - 373
241HH-2 - 3701 - 373
142EE-2 - 3681 - 371
242II-2 - 3681 - 371
143EE-2 - 3701 - 373
243JJ-2 - 3701 - 373
144EE-2 - 3701 - 373
244KK-2 - 3701 - 373
145EE-2 - 3681 - 371
245LL-2 - 3681 - 371
146FF-2 - 3701 - 373
246GG-2 - 3701 - 373
147FF-2 - 3701 - 373
247HH-2 - 3701 - 373
148FF-2 - 3681 - 371
248II-2 - 3681 - 371
149FF-2 - 3701 - 373
249JJ-2 - 3701 - 373
150FF-2 - 3701 - 373
250KK-2 - 3701 - 373
151FF-2 - 3681 - 371
251LL-2 - 3681 - 371
152GG-2 - 3701 - 373
252HH-2 - 3701 - 373
153GG-2 - 3681 - 371
253II-2 - 3681 - 371
154GG-2 - 3701 - 373
254JJ-2 - 3701 - 373
155GG-2 - 3701 - 373
255KK-2 - 3701 - 373
156GG-2 - 3681 - 371
256LL-2 - 3681 - 371
157HH-2 - 3681 - 371
257II-2 - 3681 - 371
158HH-2 - 3701 - 373
258JJ-2 - 3701 - 373
159HH-2 - 3701 - 373
259KK-2 - 3701 - 373
160HH-2 - 3681 - 371
260LL-2 - 3681 - 371
161II-2 - 3681 - 371
261JJ-2 - 3681 - 371
162II-2 - 3681 - 371
262KK-2 - 3681 - 371
163II-2 - 3691 - 372
263LL-2 - 3691 - 372
164JJ-2 - 3701 - 373
264KK-2 - 3701 - 373
165JJ-2 - 3681 - 371
265LL-2 - 3681 - 371
166KK-2 - 3681 - 371
266LL-2 - 3681 - 371

NCS ensembles :
ID
1
2
3
4
5
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Components

-
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

-
Non-polymers , 4 types, 291 molecules

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


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


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


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


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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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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