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- PDB-6tqd: D00-D0 domain of Intimin -

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Basic information

Entry
Database: PDB / ID: 6tqd
TitleD00-D0 domain of Intimin
ComponentsIntimin
KeywordsCELL ADHESION / intimin / adhesion / passenger domain / bacterial Ig domain / BIG domain
Function / homology
Function and homology information


cell outer membrane / cell adhesion
Similarity search - Function
Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / : / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain ...Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / : / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Bacterial Ig-like domain 2 / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2 / Lysin motif / LysM domain / LysM domain profile. / LysM domain / C-type lectin-like/link domain superfamily / C-type lectin fold / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Intimin
Similarity search - Component
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsWeikum, J. / Leo, J.C. / Morth, J.P.
CitationJournal: Sci Rep / Year: 2020
Title: The extracellular juncture domains in the intimin passenger adopt a constitutively extended conformation inducing restraints to its sphere of action.
Authors: Weikum, J. / Kulakova, A. / Tesei, G. / Yoshimoto, S. / Jaegerum, L.V. / Schutz, M. / Hori, K. / Skepo, M. / Harris, P. / Leo, J.C. / Morth, J.P.
History
DepositionDec 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 15, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Feb 7, 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
A: Intimin
B: Intimin
C: Intimin
D: Intimin
E: Intimin
F: Intimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,52224
Polymers130,3506
Non-polymers1,17218
Water36,7332039
1
A: Intimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0147
Polymers21,7251
Non-polymers2896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9435
Polymers21,7251
Non-polymers2184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Intimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9204
Polymers21,7251
Non-polymers1953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Intimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0354
Polymers21,7251
Non-polymers3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Intimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8052
Polymers21,7251
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Intimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8052
Polymers21,7251
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.039, 65.473, 79.378
Angle α, β, γ (deg.)77.776, 76.550, 84.762
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELEULEU(chain 'A' and (resid 453 through 456 or resid 458...AA453 - 4565 - 8
12ILEILEGLUGLU(chain 'A' and (resid 453 through 456 or resid 458...AA458 - 46610 - 18
13SERSERGLNGLN(chain 'A' and (resid 453 through 456 or resid 458...AA468 - 47020 - 22
14ILEILELEULEU(chain 'A' and (resid 453 through 456 or resid 458...AA472 - 47424 - 26
15VALVALVALVAL(chain 'A' and (resid 453 through 456 or resid 458...AA47628
16SERSERILEILE(chain 'A' and (resid 453 through 456 or resid 458...AA478 - 48530 - 37
17TRPTRPASPASP(chain 'A' and (resid 453 through 456 or resid 458...AA487 - 48939 - 41
18ALAALAARGARG(chain 'A' and (resid 453 through 456 or resid 458...AA491 - 49343 - 45
19GLNGLNGLNGLN(chain 'A' and (resid 453 through 456 or resid 458...AA495 - 49847 - 50
110GLNGLNGLNGLN(chain 'A' and (resid 453 through 456 or resid 458...AA50052
111SERSERSERSER(chain 'A' and (resid 453 through 456 or resid 458...AA502 - 50454 - 56
112SERSERGLNGLN(chain 'A' and (resid 453 through 456 or resid 458...AA506 - 50858 - 60
113TYRTYRVALVAL(chain 'A' and (resid 453 through 456 or resid 458...AA510 - 51862 - 70
114GLYGLYASPASP(chain 'A' and (resid 453 through 456 or resid 458...AA520 - 53372 - 85
115ASNASNVALVAL(chain 'A' and (resid 453 through 456 or resid 458...AA535 - 54887 - 100
116SERSERSERSER(chain 'A' and (resid 453 through 456 or resid 458...AA550102
117GLYGLYSERSER(chain 'A' and (resid 453 through 456 or resid 458...AA552 - 569104 - 121
118ALAALAGLNGLN(chain 'A' and (resid 453 through 456 or resid 458...AA572 - 591124 - 143
119VALVALVALVAL(chain 'A' and (resid 453 through 456 or resid 458...AA594 - 596146 - 148
120PHEPHEPHEPHE(chain 'A' and (resid 453 through 456 or resid 458...AA598150
121ILEILESERSER(chain 'A' and (resid 453 through 456 or resid 458...AA600 - 608152 - 160
122ALAALAASPASP(chain 'A' and (resid 453 through 456 or resid 458...AA612 - 627164 - 179
123PROPROASNASN(chain 'A' and (resid 453 through 456 or resid 458...AA629 - 646181 - 198
124ALAALAASPASP(chain 'A' and (resid 453 through 456 or resid 458...AA649 - 654201 - 206
225ILEILELEULEU(chain 'B' and (resid 453 through 456 or resid 458...BB453 - 4565 - 8
226ILEILEGLUGLU(chain 'B' and (resid 453 through 456 or resid 458...BB458 - 46610 - 18
227SERSERGLNGLN(chain 'B' and (resid 453 through 456 or resid 458...BB468 - 47020 - 22
228ILEILELEULEU(chain 'B' and (resid 453 through 456 or resid 458...BB472 - 47424 - 26
229VALVALVALVAL(chain 'B' and (resid 453 through 456 or resid 458...BB47628
230SERSERILEILE(chain 'B' and (resid 453 through 456 or resid 458...BB478 - 48530 - 37
231TRPTRPASPASP(chain 'B' and (resid 453 through 456 or resid 458...BB487 - 48939 - 41
232ALAALAARGARG(chain 'B' and (resid 453 through 456 or resid 458...BB491 - 49343 - 45
233GLNGLNGLNGLN(chain 'B' and (resid 453 through 456 or resid 458...BB495 - 49847 - 50
234GLNGLNGLNGLN(chain 'B' and (resid 453 through 456 or resid 458...BB50052
235SERSERSERSER(chain 'B' and (resid 453 through 456 or resid 458...BB502 - 50454 - 56
236SERSERGLNGLN(chain 'B' and (resid 453 through 456 or resid 458...BB506 - 50858 - 60
237TYRTYRVALVAL(chain 'B' and (resid 453 through 456 or resid 458...BB510 - 51862 - 70
238GLYGLYASPASP(chain 'B' and (resid 453 through 456 or resid 458...BB520 - 53372 - 85
239ASNASNVALVAL(chain 'B' and (resid 453 through 456 or resid 458...BB535 - 54887 - 100
240SERSERSERSER(chain 'B' and (resid 453 through 456 or resid 458...BB550102
241GLYGLYSERSER(chain 'B' and (resid 453 through 456 or resid 458...BB552 - 569104 - 121
242ALAALAGLNGLN(chain 'B' and (resid 453 through 456 or resid 458...BB572 - 591124 - 143
243VALVALVALVAL(chain 'B' and (resid 453 through 456 or resid 458...BB594 - 596146 - 148
244PHEPHEPHEPHE(chain 'B' and (resid 453 through 456 or resid 458...BB598150
245ILEILESERSER(chain 'B' and (resid 453 through 456 or resid 458...BB600 - 608152 - 160
246ALAALAASPASP(chain 'B' and (resid 453 through 456 or resid 458...BB612 - 627164 - 179
247PROPROASNASN(chain 'B' and (resid 453 through 456 or resid 458...BB629 - 646181 - 198
248ALAALAASPASP(chain 'B' and (resid 453 through 456 or resid 458...BB649 - 654201 - 206
349ILEILELEULEU(chain 'C' and (resid 453 through 456 or resid 458...CC453 - 4565 - 8
350ILEILEGLUGLU(chain 'C' and (resid 453 through 456 or resid 458...CC458 - 46610 - 18
351SERSERGLNGLN(chain 'C' and (resid 453 through 456 or resid 458...CC468 - 47020 - 22
352ILEILELEULEU(chain 'C' and (resid 453 through 456 or resid 458...CC472 - 47424 - 26
353VALVALVALVAL(chain 'C' and (resid 453 through 456 or resid 458...CC47628
354SERSERILEILE(chain 'C' and (resid 453 through 456 or resid 458...CC478 - 48530 - 37
355TRPTRPASPASP(chain 'C' and (resid 453 through 456 or resid 458...CC487 - 48939 - 41
356ALAALAARGARG(chain 'C' and (resid 453 through 456 or resid 458...CC491 - 49343 - 45
357GLNGLNGLNGLN(chain 'C' and (resid 453 through 456 or resid 458...CC495 - 49847 - 50
358GLNGLNGLNGLN(chain 'C' and (resid 453 through 456 or resid 458...CC50052
359SERSERSERSER(chain 'C' and (resid 453 through 456 or resid 458...CC502 - 50454 - 56
360SERSERGLNGLN(chain 'C' and (resid 453 through 456 or resid 458...CC506 - 50858 - 60
361TYRTYRVALVAL(chain 'C' and (resid 453 through 456 or resid 458...CC510 - 51862 - 70
362GLYGLYASPASP(chain 'C' and (resid 453 through 456 or resid 458...CC520 - 53372 - 85
363ASNASNVALVAL(chain 'C' and (resid 453 through 456 or resid 458...CC535 - 54887 - 100
364SERSERSERSER(chain 'C' and (resid 453 through 456 or resid 458...CC550102
365GLYGLYSERSER(chain 'C' and (resid 453 through 456 or resid 458...CC552 - 569104 - 121
366ALAALAGLNGLN(chain 'C' and (resid 453 through 456 or resid 458...CC572 - 591124 - 143
367VALVALVALVAL(chain 'C' and (resid 453 through 456 or resid 458...CC594 - 596146 - 148
368PHEPHEPHEPHE(chain 'C' and (resid 453 through 456 or resid 458...CC598150
369ILEILESERSER(chain 'C' and (resid 453 through 456 or resid 458...CC600 - 608152 - 160
370ALAALAASPASP(chain 'C' and (resid 453 through 456 or resid 458...CC612 - 627164 - 179
371PROPROASNASN(chain 'C' and (resid 453 through 456 or resid 458...CC629 - 646181 - 198
372ALAALAASPASP(chain 'C' and (resid 453 through 456 or resid 458...CC649 - 654201 - 206
473ILEILELEULEU(chain 'D' and (resid 453 through 456 or resid 458...DD453 - 4565 - 8
474ILEILEGLUGLU(chain 'D' and (resid 453 through 456 or resid 458...DD458 - 46610 - 18
475SERSERGLNGLN(chain 'D' and (resid 453 through 456 or resid 458...DD468 - 47020 - 22
476ILEILELEULEU(chain 'D' and (resid 453 through 456 or resid 458...DD472 - 47424 - 26
477VALVALVALVAL(chain 'D' and (resid 453 through 456 or resid 458...DD47628
478SERSERILEILE(chain 'D' and (resid 453 through 456 or resid 458...DD478 - 48530 - 37
479TRPTRPASPASP(chain 'D' and (resid 453 through 456 or resid 458...DD487 - 48939 - 41
480ALAALAARGARG(chain 'D' and (resid 453 through 456 or resid 458...DD491 - 49343 - 45
481GLNGLNGLNGLN(chain 'D' and (resid 453 through 456 or resid 458...DD495 - 49847 - 50
482GLNGLNGLNGLN(chain 'D' and (resid 453 through 456 or resid 458...DD50052
483SERSERSERSER(chain 'D' and (resid 453 through 456 or resid 458...DD502 - 50454 - 56
484SERSERGLNGLN(chain 'D' and (resid 453 through 456 or resid 458...DD506 - 50858 - 60
485TYRTYRVALVAL(chain 'D' and (resid 453 through 456 or resid 458...DD510 - 51862 - 70
486GLYGLYASPASP(chain 'D' and (resid 453 through 456 or resid 458...DD520 - 53372 - 85
487ASNASNVALVAL(chain 'D' and (resid 453 through 456 or resid 458...DD535 - 54887 - 100
488SERSERSERSER(chain 'D' and (resid 453 through 456 or resid 458...DD550102
489GLYGLYSERSER(chain 'D' and (resid 453 through 456 or resid 458...DD552 - 569104 - 121
490ALAALAGLNGLN(chain 'D' and (resid 453 through 456 or resid 458...DD572 - 591124 - 143
491VALVALVALVAL(chain 'D' and (resid 453 through 456 or resid 458...DD594 - 596146 - 148
492PHEPHEPHEPHE(chain 'D' and (resid 453 through 456 or resid 458...DD598150
493ILEILESERSER(chain 'D' and (resid 453 through 456 or resid 458...DD600 - 608152 - 160
494ALAALAASPASP(chain 'D' and (resid 453 through 456 or resid 458...DD612 - 627164 - 179
495PROPROASNASN(chain 'D' and (resid 453 through 456 or resid 458...DD629 - 646181 - 198
496ALAALAASPASP(chain 'D' and (resid 453 through 456 or resid 458...DD649 - 654201 - 206
597ILEILELEULEU(chain 'E' and (resid 453 through 456 or resid 458...EE453 - 4565 - 8
598ILEILEGLUGLU(chain 'E' and (resid 453 through 456 or resid 458...EE458 - 46610 - 18
599SERSERGLNGLN(chain 'E' and (resid 453 through 456 or resid 458...EE468 - 47020 - 22
5100ILEILELEULEU(chain 'E' and (resid 453 through 456 or resid 458...EE472 - 47424 - 26
5101VALVALVALVAL(chain 'E' and (resid 453 through 456 or resid 458...EE47628
5102SERSERILEILE(chain 'E' and (resid 453 through 456 or resid 458...EE478 - 48530 - 37
5103TRPTRPASPASP(chain 'E' and (resid 453 through 456 or resid 458...EE487 - 48939 - 41
5104ALAALAARGARG(chain 'E' and (resid 453 through 456 or resid 458...EE491 - 49343 - 45
5105GLNGLNGLNGLN(chain 'E' and (resid 453 through 456 or resid 458...EE495 - 49847 - 50
5106GLNGLNGLNGLN(chain 'E' and (resid 453 through 456 or resid 458...EE50052
5107SERSERSERSER(chain 'E' and (resid 453 through 456 or resid 458...EE502 - 50454 - 56
5108SERSERGLNGLN(chain 'E' and (resid 453 through 456 or resid 458...EE506 - 50858 - 60
5109TYRTYRVALVAL(chain 'E' and (resid 453 through 456 or resid 458...EE510 - 51862 - 70
5110GLYGLYASPASP(chain 'E' and (resid 453 through 456 or resid 458...EE520 - 53372 - 85
5111ASNASNVALVAL(chain 'E' and (resid 453 through 456 or resid 458...EE535 - 54887 - 100
5112SERSERSERSER(chain 'E' and (resid 453 through 456 or resid 458...EE550102
5113GLYGLYSERSER(chain 'E' and (resid 453 through 456 or resid 458...EE552 - 569104 - 121
5114ALAALAGLNGLN(chain 'E' and (resid 453 through 456 or resid 458...EE572 - 591124 - 143
5115VALVALVALVAL(chain 'E' and (resid 453 through 456 or resid 458...EE594 - 596146 - 148
5116PHEPHEPHEPHE(chain 'E' and (resid 453 through 456 or resid 458...EE598150
5117ILEILESERSER(chain 'E' and (resid 453 through 456 or resid 458...EE600 - 608152 - 160
5118ALAALAASPASP(chain 'E' and (resid 453 through 456 or resid 458...EE612 - 627164 - 179
5119PROPROASNASN(chain 'E' and (resid 453 through 456 or resid 458...EE629 - 646181 - 198
5120ALAALAASPASP(chain 'E' and (resid 453 through 456 or resid 458...EE649 - 654201 - 206
6121ILEILELEULEU(chain 'F' and (resid 453 through 456 or resid 458...FF453 - 4565 - 8
6122ILEILEGLUGLU(chain 'F' and (resid 453 through 456 or resid 458...FF458 - 46610 - 18
6123SERSERGLNGLN(chain 'F' and (resid 453 through 456 or resid 458...FF468 - 47020 - 22
6124ILEILELEULEU(chain 'F' and (resid 453 through 456 or resid 458...FF472 - 47424 - 26
6125VALVALVALVAL(chain 'F' and (resid 453 through 456 or resid 458...FF47628
6126SERSERILEILE(chain 'F' and (resid 453 through 456 or resid 458...FF478 - 48530 - 37
6127TRPTRPASPASP(chain 'F' and (resid 453 through 456 or resid 458...FF487 - 48939 - 41
6128ALAALAARGARG(chain 'F' and (resid 453 through 456 or resid 458...FF491 - 49343 - 45
6129GLNGLNGLNGLN(chain 'F' and (resid 453 through 456 or resid 458...FF495 - 49847 - 50
6130GLNGLNGLNGLN(chain 'F' and (resid 453 through 456 or resid 458...FF50052
6131SERSERSERSER(chain 'F' and (resid 453 through 456 or resid 458...FF502 - 50454 - 56
6132SERSERGLNGLN(chain 'F' and (resid 453 through 456 or resid 458...FF506 - 50858 - 60
6133TYRTYRVALVAL(chain 'F' and (resid 453 through 456 or resid 458...FF510 - 51862 - 70
6134GLYGLYASPASP(chain 'F' and (resid 453 through 456 or resid 458...FF520 - 53372 - 85
6135ASNASNVALVAL(chain 'F' and (resid 453 through 456 or resid 458...FF535 - 54887 - 100
6136SERSERSERSER(chain 'F' and (resid 453 through 456 or resid 458...FF550102
6137GLYGLYSERSER(chain 'F' and (resid 453 through 456 or resid 458...FF552 - 569104 - 121
6138ALAALAGLNGLN(chain 'F' and (resid 453 through 456 or resid 458...FF572 - 591124 - 143
6139VALVALVALVAL(chain 'F' and (resid 453 through 456 or resid 458...FF594 - 596146 - 148
6140PHEPHEPHEPHE(chain 'F' and (resid 453 through 456 or resid 458...FF598150
6141ILEILESERSER(chain 'F' and (resid 453 through 456 or resid 458...FF600 - 608152 - 160
6142ALAALAASPASP(chain 'F' and (resid 453 through 456 or resid 458...FF612 - 627164 - 179
6143PROPROASNASN(chain 'F' and (resid 453 through 456 or resid 458...FF629 - 646181 - 198
6144ALAALAASPASP(chain 'F' and (resid 453 through 456 or resid 458...FF649 - 654201 - 206

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Intimin / Attaching and effacing protein / Eae protein


Mass: 21725.047 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 str. E2348/69 (bacteria)
Gene: eae, eaeA, E2348C_3939 / Production host: Escherichia coli (E. coli) / References: UniProt: P19809

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Non-polymers , 5 types, 2057 molecules

#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2039 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: D00-D0 50 mg/ml. in 400mM NaCl 10 mM Hepes pH 7.5. Reservoir solution 150 mM KBr. 30% PEG2000mme

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.479→24.83 Å / Num. obs: 175969 / % possible obs: 98.18 % / Redundancy: 4.6 % / Biso Wilson estimate: 10.72 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.1293 / Net I/σ(I): 6.4
Reflection shellResolution: 1.479→1.532 Å / Rmerge(I) obs: 0.5734 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 16162 / CC1/2: 0.354 / Rrim(I) all: 0.6962

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f00

1f00


Resolution: 1.48→24.83 Å / SU ML: 0.1644 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.1479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2155 8656 4.93 %
Rwork0.1789 167067 -
obs0.1807 175723 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.88 Å2
Refinement stepCycle: LAST / Resolution: 1.48→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9045 0 30 2039 11114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059443
X-RAY DIFFRACTIONf_angle_d0.70812891
X-RAY DIFFRACTIONf_chiral_restr0.07841560
X-RAY DIFFRACTIONf_plane_restr0.00441713
X-RAY DIFFRACTIONf_dihedral_angle_d15.88773394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.34082410.33084921X-RAY DIFFRACTION85.8
1.5-1.510.41222650.37515045X-RAY DIFFRACTION89.45
1.51-1.530.29242600.27995411X-RAY DIFFRACTION95.36
1.53-1.550.2853160.2665397X-RAY DIFFRACTION94.68
1.55-1.570.31382630.28065436X-RAY DIFFRACTION97.02
1.57-1.590.27312760.24085596X-RAY DIFFRACTION98.26
1.59-1.620.28482530.22895632X-RAY DIFFRACTION98.87
1.62-1.640.26012880.22235681X-RAY DIFFRACTION99.24
1.64-1.670.2543150.21855590X-RAY DIFFRACTION99.21
1.67-1.690.26752940.20975581X-RAY DIFFRACTION99.22
1.69-1.720.24933090.19855646X-RAY DIFFRACTION99.33
1.72-1.750.23782920.19835641X-RAY DIFFRACTION99.2
1.75-1.790.23612770.19785638X-RAY DIFFRACTION99.11
1.79-1.820.24682930.1975614X-RAY DIFFRACTION98.94
1.82-1.860.20733010.17575642X-RAY DIFFRACTION99.35
1.86-1.910.19482960.1695592X-RAY DIFFRACTION99.59
1.91-1.950.20693040.1685667X-RAY DIFFRACTION99.5
1.95-2.010.21443080.17035611X-RAY DIFFRACTION99.63
2.01-2.070.1992850.16425630X-RAY DIFFRACTION99.6
2.07-2.130.19443060.1645660X-RAY DIFFRACTION99.52
2.13-2.210.19132830.16135610X-RAY DIFFRACTION99.23
2.21-2.30.21823120.16465647X-RAY DIFFRACTION99.67
2.3-2.40.22133090.16295642X-RAY DIFFRACTION99.56
2.4-2.530.20792860.15995649X-RAY DIFFRACTION99.58
2.53-2.690.20913050.16035623X-RAY DIFFRACTION99.75
2.69-2.890.19322870.16065654X-RAY DIFFRACTION99.7
2.89-3.180.1822680.15945679X-RAY DIFFRACTION99.7
3.18-3.640.19622690.15215684X-RAY DIFFRACTION99.7
3.64-4.590.18143050.14195655X-RAY DIFFRACTION99.72
4.59-24.830.17862900.16745593X-RAY DIFFRACTION98.66
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)
10.4454117720.1805557066880.05713629128490.390477423298-0.02616141704160.02005282780550.0545971426705-0.06917578001330.1444674983510.0849957221642-0.03404556335860.107460442023-0.08966755255310.04001781999870.02090203593530.080225445673-0.02998681597250.01051319160490.109485772104-0.02475653077250.0619623038425-11.722894280931.07110545573.47559838808
20.2429796652770.0730591736923-0.01296263905350.0514691586719-0.00253130534170.268944919181-0.03807002863070.0919483601810.164743371837-0.08453632972210.02427124074270.117500947704-0.123546839321-0.1561195088580.07319878309890.09128598316720.000765383008406-0.01885625093740.1434866278160.01421882581980.139124071362-16.81848080728.6116996835-3.13450868361
31.498718576441.026648095680.542678710381.044776548640.4939565708190.65662039804-0.1916286826960.1561289431260.195881613071-0.2376134800620.03662137181940.125483339194-0.195523048880.00754395001727-0.7367542117460.101696757476-0.01126545593450.00333091499010.08818855383760.01204797819640.0432313730687-9.6724636270227.0405817711-7.34743293505
40.8007312548160.09932588260710.03401984356360.122283242616-0.07440727197860.125044551796-0.01366646837280.00769695196264-0.4344736133980.10167853083-0.00436001416283-0.02553202331710.258387164458-0.2734419127630.006068538360290.122628561278-0.03721338700920.01105552370130.114949051719-0.003260032639620.141845565131-22.250172054711.1379790567-0.699479372377
50.2152362294620.0557197764909-0.04791651563010.6137170662150.2201828488930.248188848167-0.001341166953330.0507338907618-0.026354309719-0.00816653761691-0.05552462637630.0784084400254-0.0238275460426-0.0223043746599-0.8824176041650.0632653298795-0.02334707082630.004224280679140.0806331191435-0.00467882338839-0.00443001287276-6.7214746308926.43206169870.177679405219
60.962139076109-0.05340836224810.006003124517620.552362890199-0.3578150510070.6993587423220.000156866648793-0.0337488922017-0.299144349695-0.1931564159110.0715600145060.1396036103160.1872574831950.07746087544830.8630549082330.116157557994-0.00284136438008-0.002724719278050.09042068141060.04814526264670.112499703104-37.43003053256.7317144277611.6722326117
70.319569466978-0.3586486156940.03747269551450.4130550502210.02978444488160.4019061914020.0385445415714-0.114630641984-0.270018603431-0.01583794553990.04401916088420.2724735934190.171961648266-0.02895791373730.2524033597440.12616618354-0.0223364664341-0.02727744384450.1202069250050.1080993851420.181501408642-39.45468280152.9708450467616.534728642
80.306642772462-0.0793107087828-0.2036704061810.1689022474490.07615164373490.158988026840.00465399818640.0620099838453-0.187923545789-0.2670897486740.09028386508390.26903140140.264515979285-0.1081885814790.3149661552030.265994984308-0.0324822545034-0.08545636517110.09294125613880.03038951030060.184782079516-42.31532242713.608383455186.92878647751
90.5590833224970.1745839292790.06848949310550.384496577458-0.1236662374940.101128909320.0836011703901-0.09663516968460.1146300235190.0726676989442-0.03378493594940.136227368647-0.04713896175440.06019946775010.04980516739190.0750163147759-0.03266405533890.01967405239030.109019466081-0.01968429006110.0872123478771-3.1023967672737.944434720928.9707125643
100.0806331613372-0.0947607209927-0.0144597989260.1096799181650.02023903940210.003884837701820.0343756373041-0.1329026851640.113584177916-0.0295604276876-0.07014856713590.123177252385-0.0756784215215-0.07529981832790.01831153614410.0831999104858-0.00881994315180.01059696324350.0981092886156-0.006735875714780.129746436645-9.8619246399134.218330722621.1622480333
110.7664531893020.0278909938502-0.1325758483320.239991870644-0.08501827361460.089240952268-0.03702671001490.0447968836954-0.21447381556-0.0852749782175-0.004503700236180.0451071147348-0.030473658689-0.00498215554474-0.1878992456440.105380421168-0.0207956905747-0.01603881366480.06199075939160.001793368187030.0894485763129-5.41523370529.212666330918.2137265142
120.429571407866-0.194436877924-0.07205588824970.08718782855850.03016578045710.0255015358946-0.00318493347545-0.0457166493949-0.1418539926950.00957334599631-0.01321310969890.0236415521843-0.03147897481050.041991376939-0.1107738350470.0388514063014-0.0254031332355-0.005782356856260.05945956262150.005183447289460.0404965685052-0.98419880325730.868163208324.7458117361
130.524566063632-0.0426774823131-0.4030616928870.459129572426-0.3015384546280.557744091539-0.1418068571-0.4276799689-0.188541342584-0.02256179844660.00454422297476-0.1764694202010.1029332936370.213126419906-0.7447193623830.08018131471730.0279765574610.04062896629080.1287450682250.0668511919880.104555059125-32.08849809111.02464754935.3766267845
140.8327881289640.31820896561-0.01935049942980.3612496868090.122275823230.32982772733-0.124041529376-0.263015884065-0.0567087897218-0.12361576404-0.106354648087-0.1112596646920.2783408426570.0996770104841-2.039962242450.1775781665810.01986246912450.04159950877660.1292394990380.06157517798450.0863909415995-35.9246778697.6370489446334.7211801315
150.02678256025980.02292863801250.007043746429020.0182820480168-0.00372377719820.01489516674460.153293789154-0.1209005460140.1449132010320.120182926546-0.1395033941610.14373788449-0.06098342983770.007437370016280.004731615317730.17540414133-0.03888085121340.03717916196790.146785325089-0.01181706752530.16806673029-0.5962887515941.116528353252.3295005445
160.05043066737940.0325071767667-0.02024342785440.0216443853659-0.01850528223490.0199232506320.00729405016309-0.0505705135350.199976935684-0.107500711586-0.08560383668060.190986751207-0.0933908121848-0.08075870502450.0005901074197990.121424595586-0.007162519909890.01212290681630.1078640727830.008306675090720.213466654804-4.6314781070839.082516801245.3136836074
170.210226153259-0.0549823781063-0.03800986014210.01625839041850.02538563501940.159781708316-0.1100487757440.0707872001368-0.0910279333083-0.1228518335430.00715837617510.07832889467320.0003876048663810.153333162544-0.70762317620.0882625251591-0.0239297864658-0.009469383794560.05610457552620.006761766810060.09310512286614.6744921335235.386554556943.1911323836
180.0109187018177-0.014826921791-0.003881465157230.01808860015820.003623761111240.0008633138291680.04826446449690.07157448510450.232480505154-0.329526313445-0.08273842287230.0282358403089-0.5037779277770.1555197886720.03716047038410.267071777031-0.0402496402982-0.004369173158360.1091369939050.01497959464920.192154254993-1.0128109310441.893152687639.1692205346
190.673858929327-0.3456288238850.08393645340520.8593574380420.2617243351650.151609236159-0.02786430449540.0240345061968-0.2472608953120.0447570845139-0.02162301146630.172166624697-0.002752538297790.0176003138937-0.1256935696270.0850861712522-0.01835301509430.007536389300760.08045950350560.008531398537350.051057090817-1.9689751749628.428032415448.5079039972
200.4741183266340.05284962267930.2012757312720.6483802982110.1675493735640.1154068974980.0935712210295-0.0206162829995-0.0171866074850.145939256344-0.0948004269890.1040016610310.03384687037990.00647932662221-0.07200870110870.0889349004011-0.03245839639510.0005276781838830.1097693037870.003376223638610.05783918772914.5512247624937.712268909450.0238485753
210.503856777965-0.207484849890.02818637250470.247511597999-0.1065068311730.3844800457350.0308971796961-0.1501214943120.04454589484520.1342153671630.01226456102690.126351288101-0.09281423001490.02002188354010.008244048760160.1476565545070.02310979195060.04986418404760.150684133791-0.0004204258596090.1387433625-26.821081323216.018958280559.3388834123
220.488833097154-0.2421035633090.2284723566820.239514943154-0.3488288933620.574240140541-0.0643424361708-0.228296501973-0.1774284271280.1427590487270.06964522047510.0854155637125-0.1453218262050.1233674093020.003830366778070.1206785141770.01993786516930.0418199091530.1922477752070.01137440527340.109094946718-29.191519981312.516349814564.7596814335
230.8484003350840.2842563206380.3311942878470.09836000651850.1286655801910.461363619468-0.07155204822840.07792786979140.239283731512-0.04115232009190.02337410303790.203423332981-0.134272128043-0.11582226643-0.08295812013570.1298909168490.03158650051770.02421540367630.1372141008960.01236517354050.119635775064-31.690846171912.518292767154.8046526317
240.698998376254-0.181372825537-0.3625434275490.1048117147440.1573127975370.7206323485230.1048497535920.07432004160820.1753835773270.0228370988673-0.00516071748407-0.05054467476390.0906568315497-0.01767163972591.646907576250.0759801262413-0.01129266116650.01074797041240.1301291870370.04847137418930.0378587781948-28.093642729245.710101675853.0716685105
250.760373113434-0.026562924321-0.130845039360.565990045237-0.04074158455150.348479822334-0.0248510399832-0.002907811105560.06974739530870.01114879639050.006209449443560.0289595624785-0.0423461422294-0.0473218638973-0.09807681082420.06239685377430.00337663156423-0.003255272563350.0402282011182-0.02199217665030.07389722502531.9467143992368.311130148543.4491923298
260.7342521683070.484027901141-0.2381690774640.5615237448250.1183686433540.425327563160.14694024436-0.200828104039-0.3806346870660.03795480458710.0566315597764-0.1500387224040.0951717795679-0.05608400869052.057272317140.0858202968909-0.0149764589298-0.01560813728130.1885889355460.08872710747870.205122741426-28.592062817638.125454307628.9993355427
270.5378821637890.267338061842-0.002645662291080.6994129645020.08447252040120.583848543722-0.00182888098802-0.08308560325290.0916391684524-0.152316919334-0.0288633472139-0.0218902168319-0.00623864855904-0.0513169557251-0.3180366957250.0573727742018-0.0121873855385-0.008298034111580.0685708833510.0390775497010.0975741442733-38.252566208640.697856345925.5709959875
280.9514598950020.1651807470360.9382798608080.1192733625380.1557408760210.9288258654030.1427492850.00186832496618-0.353790800423-0.1274856786610.0608590412870.1348360789380.494212879839-0.07618906688520.2699213425580.215108834288-0.006120446785680.01608918603930.0944587797231-0.0183966573230.207532954087-33.992059954732.86681045322.2321457017
290.547672305277-0.250776018555-0.1473553158020.5610874347050.3220174631030.2149833427640.0463180899066-0.07454335138080.1539564902-0.06574375651390.065753997102-0.0528578338076-0.0211861406085-0.1404343459820.8501156460580.0477929529873-0.0266199746229-0.02092645518970.1637475897080.02611647122920.0492704977742-32.760015299745.34018878728.6300237939
300.2206860400690.2104967581990.1480610357660.2127463389560.1189440087660.133039004881-0.178102569046-0.1265067063950.387928956544-0.111063118185-0.05153029093410.105166453525-0.110637937054-0.108468878107-2.351585321350.0975460050817-0.0570943613821-0.08965013797260.0129201772825-0.03943655879060.37970716738-4.5144716110462.195280829420.1599705372
310.4493561317250.263445649590.2212643907770.536171401337-0.2778724933070.657916333827-0.188522322366-0.08442930879110.348934222373-0.233171427949-0.1091524647570.243552435367-0.190030391676-0.0219695103623-3.003061350810.204220943296-0.0148425769804-0.1187316673840.0266974941198-0.03422517081880.342276371477-1.5365493938264.0601977217.4371742439
320.21386858409-0.04203324152170.05881860842360.2805795128710.1130228493410.07213158932430.0244530861156-0.0387496563029-0.07022567694070.0463548442277-0.105458473682-0.133066947332-0.03163406608590.08026303199248.39254375638E-50.098479417061-0.01035045394650.01050107161570.1066128462150.03341841613170.122366648175-35.802968277133.110932033.55426752652
330.625366818328-0.425406971910.1035123941710.725402315182-0.1808589197560.6853614787350.04434067366510.06708905562320.246297418125-0.0955942577323-0.133998554433-0.2130716635850.02227494052130.0601890096183-0.8624103453380.0818333982543-0.01001142593680.03433356271260.03839764615860.02538718904920.0110293767294-41.504561019237.0244848923-0.864809836822
340.6011199277770.149368553474-0.2112475851450.646230999431-0.4127457960670.2907032620930.0102082393302-0.0632513820670.0657967889523-0.00689408564559-0.12855898935-0.0746642602565-0.09225110001680.108940173207-0.8601704788380.107966958862-0.03848320141630.02085333777260.110491356052-0.00804557347460.064138544453-41.671383451836.24687422736.64598792988
350.204765951817-0.115757040189-0.1331085850090.461665958840.2904664406590.1914065050460.00729661386258-0.0624916605598-0.09717518817080.02309261089690.0507070344552-0.2345999202670.04759544011370.01419934453390.0001080510900050.155155770194-0.00690650963624-0.03023440062140.166031791328-0.002324891099390.198347256865-11.799213773757.3791362487-7.12420372924
361.35964244232-1.01318758406-0.3827800415461.049934537190.09103543735140.2514197716270.182972175849-0.1121281287180.1783174396080.00222973602851-0.00996372458068-0.3201449325590.08149519393210.1669657057880.4473869597010.209818874561-0.0530037735926-0.04893275327590.167894492241-0.04838678837330.165490072564-7.8630318229262.3135004327-5.06346498723
370.486632206527-0.0831674746923-0.1892430649210.02536318573730.05683327220750.122529380633-0.04487647243070.148168233827-0.15922392624-0.2811502401990.0281659057621-0.003488185802410.11735578352-0.0443394444939-0.01701203486840.2765564370850.00154463294396-0.01819611091650.194389181646-0.02148033764110.147375338715-10.105075767859.0715044995-14.2447612405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 452 through 465 )
2X-RAY DIFFRACTION2chain 'A' and (resid 466 through 478 )
3X-RAY DIFFRACTION3chain 'A' and (resid 479 through 513 )
4X-RAY DIFFRACTION4chain 'A' and (resid 514 through 523 )
5X-RAY DIFFRACTION5chain 'A' and (resid 524 through 549 )
6X-RAY DIFFRACTION6chain 'A' and (resid 550 through 610 )
7X-RAY DIFFRACTION7chain 'A' and (resid 611 through 629 )
8X-RAY DIFFRACTION8chain 'A' and (resid 630 through 655 )
9X-RAY DIFFRACTION9chain 'B' and (resid 450 through 465 )
10X-RAY DIFFRACTION10chain 'B' and (resid 466 through 478 )
11X-RAY DIFFRACTION11chain 'B' and (resid 479 through 523 )
12X-RAY DIFFRACTION12chain 'B' and (resid 524 through 549 )
13X-RAY DIFFRACTION13chain 'B' and (resid 550 through 610 )
14X-RAY DIFFRACTION14chain 'B' and (resid 611 through 655 )
15X-RAY DIFFRACTION15chain 'C' and (resid 452 through 465 )
16X-RAY DIFFRACTION16chain 'C' and (resid 466 through 478 )
17X-RAY DIFFRACTION17chain 'C' and (resid 479 through 501 )
18X-RAY DIFFRACTION18chain 'C' and (resid 502 through 513 )
19X-RAY DIFFRACTION19chain 'C' and (resid 514 through 533 )
20X-RAY DIFFRACTION20chain 'C' and (resid 534 through 549 )
21X-RAY DIFFRACTION21chain 'C' and (resid 550 through 610 )
22X-RAY DIFFRACTION22chain 'C' and (resid 611 through 629 )
23X-RAY DIFFRACTION23chain 'C' and (resid 630 through 655 )
24X-RAY DIFFRACTION24chain 'D' and (resid 450 through 549 )
25X-RAY DIFFRACTION25chain 'D' and (resid 550 through 655 )
26X-RAY DIFFRACTION26chain 'E' and (resid 453 through 478 )
27X-RAY DIFFRACTION27chain 'E' and (resid 479 through 501 )
28X-RAY DIFFRACTION28chain 'E' and (resid 502 through 513 )
29X-RAY DIFFRACTION29chain 'E' and (resid 514 through 549 )
30X-RAY DIFFRACTION30chain 'E' and (resid 550 through 610 )
31X-RAY DIFFRACTION31chain 'E' and (resid 611 through 655 )
32X-RAY DIFFRACTION32chain 'F' and (resid 451 through 478 )
33X-RAY DIFFRACTION33chain 'F' and (resid 479 through 533 )
34X-RAY DIFFRACTION34chain 'F' and (resid 534 through 549 )
35X-RAY DIFFRACTION35chain 'F' and (resid 550 through 610 )
36X-RAY DIFFRACTION36chain 'F' and (resid 611 through 629 )
37X-RAY DIFFRACTION37chain 'F' and (resid 630 through 655 )

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