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- PDB-6ult: BRD2-BD2 in complex with the cyclic peptide 4.2_3 -

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Basic information

Entry
Database: PDB / ID: 6ult
TitleBRD2-BD2 in complex with the cyclic peptide 4.2_3
Components
  • Bromodomain-containing protein 2
  • Cyclic peptide 4.2_3
KeywordsTRANSCRIPTION/INHIBITOR / BET / bromodomain / macrocyclic peptide / BRD2 / inhibitor / RaPID / TRANSCRIPTION-INHIBITOR complex / TRANSCRIPTION
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPatel, K. / Walshe, J.L. / Walport, L.J. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1161623 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Cyclic peptides can engage a single binding pocket through highly divergent modes.
Authors: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, ...Authors: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, J.M. / Payne, R.J. / Passioura, T. / Suga, H. / Mackay, J.P.
History
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2
E: Bromodomain-containing protein 2
F: Bromodomain-containing protein 2
G: Bromodomain-containing protein 2
H: Bromodomain-containing protein 2
I: Cyclic peptide 4.2_3
J: Cyclic peptide 4.2_3
K: Cyclic peptide 4.2_3
L: Cyclic peptide 4.2_3


Theoretical massNumber of molelcules
Total (without water)109,34212
Polymers109,34212
Non-polymers00
Water1,44180
1
A: Bromodomain-containing protein 2
K: Cyclic peptide 4.2_3

C: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)27,3363
Polymers27,3363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2940 Å2
ΔGint-26 kcal/mol
Surface area12520 Å2
MethodPISA
2
B: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2

L: Cyclic peptide 4.2_3


Theoretical massNumber of molelcules
Total (without water)27,3363
Polymers27,3363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area2600 Å2
ΔGint-22 kcal/mol
Surface area13030 Å2
MethodPISA
3
E: Bromodomain-containing protein 2
J: Cyclic peptide 4.2_3

G: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)27,3363
Polymers27,3363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2790 Å2
ΔGint-21 kcal/mol
Surface area12660 Å2
MethodPISA
4
H: Bromodomain-containing protein 2
I: Cyclic peptide 4.2_3

F: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)27,3363
Polymers27,3363
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2940 Å2
ΔGint-24 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.083, 63.627, 120.339
Angle α, β, γ (deg.)90.000, 108.388, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSLEULEU(chain 'A' and (resid 353 through 357 or resid 359...AA353 - 3578 - 12
121GLUGLUSERSER(chain 'A' and (resid 353 through 357 or resid 359...AA359 - 36214 - 17
131HISHISTYRTYR(chain 'A' and (resid 353 through 357 or resid 359...AA365 - 37320 - 28
141PROPROASPASP(chain 'A' and (resid 353 through 357 or resid 359...AA375 - 37730 - 32
151GLYGLYLEULEU(chain 'A' and (resid 353 through 357 or resid 359...AA382 - 38337 - 38
161ASPASPILEILE(chain 'A' and (resid 353 through 357 or resid 359...AA385 - 39040 - 45
171HISHISVALVAL(chain 'A' and (resid 353 through 357 or resid 359...AA392 - 39947 - 54
181LYSLYSASNASN(chain 'A' and (resid 353 through 357 or resid 359...AA402 - 40557 - 60
191TYRTYRTYRTYR(chain 'A' and (resid 353 through 357 or resid 359...AA40863
1101ASPASPASPASP(chain 'A' and (resid 353 through 357 or resid 359...AA41065
1111GLUGLUVALVAL(chain 'A' and (resid 353 through 357 or resid 359...AA413 - 41868 - 73
1121LEULEUMETMET(chain 'A' and (resid 353 through 357 or resid 359...AA420 - 43875 - 93
1131LYSLYSGLUGLU(chain 'A' and (resid 353 through 357 or resid 359...AA441 - 44796 - 102
1141TYRTYRTYRTYR(chain 'A' and (resid 353 through 357 or resid 359...AA450105
211CYSCYSLEULEU(chain 'B' and (resid 353 through 357 or resid 359...BB353 - 3578 - 12
221GLUGLUSERSER(chain 'B' and (resid 353 through 357 or resid 359...BB359 - 36214 - 17
231HISHISTYRTYR(chain 'B' and (resid 353 through 357 or resid 359...BB365 - 37320 - 28
241PROPROASPASP(chain 'B' and (resid 353 through 357 or resid 359...BB375 - 37730 - 32
251GLYGLYLEULEU(chain 'B' and (resid 353 through 357 or resid 359...BB382 - 38337 - 38
261ASPASPILEILE(chain 'B' and (resid 353 through 357 or resid 359...BB385 - 39040 - 45
271HISHISVALVAL(chain 'B' and (resid 353 through 357 or resid 359...BB392 - 39947 - 54
281LYSLYSASNASN(chain 'B' and (resid 353 through 357 or resid 359...BB402 - 40557 - 60
291TYRTYRTYRTYR(chain 'B' and (resid 353 through 357 or resid 359...BB40863
2101ASPASPASPASP(chain 'B' and (resid 353 through 357 or resid 359...BB41065
2111GLUGLUVALVAL(chain 'B' and (resid 353 through 357 or resid 359...BB413 - 41868 - 73
2121LEULEUMETMET(chain 'B' and (resid 353 through 357 or resid 359...BB420 - 43875 - 93
2131LYSLYSGLUGLU(chain 'B' and (resid 353 through 357 or resid 359...BB441 - 44796 - 102
2141TYRTYRTYRTYR(chain 'B' and (resid 353 through 357 or resid 359...BB450105
311CYSCYSLEULEU(chain 'C' and (resid 353 through 357 or resid 359...CC353 - 3578 - 12
321GLUGLUSERSER(chain 'C' and (resid 353 through 357 or resid 359...CC359 - 36214 - 17
331HISHISTYRTYR(chain 'C' and (resid 353 through 357 or resid 359...CC365 - 37320 - 28
341PROPROASPASP(chain 'C' and (resid 353 through 357 or resid 359...CC375 - 37730 - 32
351GLYGLYLEULEU(chain 'C' and (resid 353 through 357 or resid 359...CC382 - 38337 - 38
361ASPASPILEILE(chain 'C' and (resid 353 through 357 or resid 359...CC385 - 39040 - 45
371HISHISVALVAL(chain 'C' and (resid 353 through 357 or resid 359...CC392 - 39947 - 54
381LYSLYSASNASN(chain 'C' and (resid 353 through 357 or resid 359...CC402 - 40557 - 60
391TYRTYRTYRTYR(chain 'C' and (resid 353 through 357 or resid 359...CC40863
3101ASPASPASPASP(chain 'C' and (resid 353 through 357 or resid 359...CC41065
3111GLUGLUVALVAL(chain 'C' and (resid 353 through 357 or resid 359...CC413 - 41868 - 73
3121LEULEUMETMET(chain 'C' and (resid 353 through 357 or resid 359...CC420 - 43875 - 93
3131LYSLYSGLUGLU(chain 'C' and (resid 353 through 357 or resid 359...CC441 - 44796 - 102
3141TYRTYRTYRTYR(chain 'C' and (resid 353 through 357 or resid 359...CC450105
411CYSCYSLEULEU(chain 'D' and (resid 353 through 357 or resid 359...DD353 - 3578 - 12
421GLUGLUSERSER(chain 'D' and (resid 353 through 357 or resid 359...DD359 - 36214 - 17
431HISHISTYRTYR(chain 'D' and (resid 353 through 357 or resid 359...DD365 - 37320 - 28
441PROPROASPASP(chain 'D' and (resid 353 through 357 or resid 359...DD375 - 37730 - 32
451GLYGLYLEULEU(chain 'D' and (resid 353 through 357 or resid 359...DD382 - 38337 - 38
461ASPASPILEILE(chain 'D' and (resid 353 through 357 or resid 359...DD385 - 39040 - 45
471HISHISVALVAL(chain 'D' and (resid 353 through 357 or resid 359...DD392 - 39947 - 54
481LYSLYSASNASN(chain 'D' and (resid 353 through 357 or resid 359...DD402 - 40557 - 60
491TYRTYRTYRTYR(chain 'D' and (resid 353 through 357 or resid 359...DD40863
4101ASPASPASPASP(chain 'D' and (resid 353 through 357 or resid 359...DD41065
4111GLUGLUVALVAL(chain 'D' and (resid 353 through 357 or resid 359...DD413 - 41868 - 73
4121LEULEUMETMET(chain 'D' and (resid 353 through 357 or resid 359...DD420 - 43875 - 93
4131LYSLYSGLUGLU(chain 'D' and (resid 353 through 357 or resid 359...DD441 - 44796 - 102
4141TYRTYRTYRTYR(chain 'D' and (resid 353 through 357 or resid 359...DD450105
511CYSCYSLEULEU(chain 'E' and (resid 353 through 357 or resid 359...EE353 - 3578 - 12
521GLUGLUSERSER(chain 'E' and (resid 353 through 357 or resid 359...EE359 - 36214 - 17
531HISHISTYRTYR(chain 'E' and (resid 353 through 357 or resid 359...EE365 - 37320 - 28
541PROPROASPASP(chain 'E' and (resid 353 through 357 or resid 359...EE375 - 37730 - 32
551GLYGLYLEULEU(chain 'E' and (resid 353 through 357 or resid 359...EE382 - 38337 - 38
561ASPASPILEILE(chain 'E' and (resid 353 through 357 or resid 359...EE385 - 39040 - 45
571HISHISVALVAL(chain 'E' and (resid 353 through 357 or resid 359...EE392 - 39947 - 54
581LYSLYSASNASN(chain 'E' and (resid 353 through 357 or resid 359...EE402 - 40557 - 60
591TYRTYRTYRTYR(chain 'E' and (resid 353 through 357 or resid 359...EE40863
5101ASPASPASPASP(chain 'E' and (resid 353 through 357 or resid 359...EE41065
5111GLUGLUVALVAL(chain 'E' and (resid 353 through 357 or resid 359...EE413 - 41868 - 73
5121LEULEUMETMET(chain 'E' and (resid 353 through 357 or resid 359...EE420 - 43875 - 93
5131LYSLYSGLUGLU(chain 'E' and (resid 353 through 357 or resid 359...EE441 - 44796 - 102
5141TYRTYRTYRTYR(chain 'E' and (resid 353 through 357 or resid 359...EE450105
611CYSCYSLEULEU(chain 'F' and (resid 353 through 357 or resid 359...FF353 - 3578 - 12
621GLUGLUSERSER(chain 'F' and (resid 353 through 357 or resid 359...FF359 - 36214 - 17
631HISHISTYRTYR(chain 'F' and (resid 353 through 357 or resid 359...FF365 - 37320 - 28
641PROPROASPASP(chain 'F' and (resid 353 through 357 or resid 359...FF375 - 37730 - 32
651GLYGLYLEULEU(chain 'F' and (resid 353 through 357 or resid 359...FF382 - 38337 - 38
661ASPASPILEILE(chain 'F' and (resid 353 through 357 or resid 359...FF385 - 39040 - 45
671HISHISVALVAL(chain 'F' and (resid 353 through 357 or resid 359...FF392 - 39947 - 54
681LYSLYSASNASN(chain 'F' and (resid 353 through 357 or resid 359...FF402 - 40557 - 60
691TYRTYRTYRTYR(chain 'F' and (resid 353 through 357 or resid 359...FF40863
6101ASPASPASPASP(chain 'F' and (resid 353 through 357 or resid 359...FF41065
6111GLUGLUVALVAL(chain 'F' and (resid 353 through 357 or resid 359...FF413 - 41868 - 73
6121LEULEUMETMET(chain 'F' and (resid 353 through 357 or resid 359...FF420 - 43875 - 93
6131LYSLYSGLUGLU(chain 'F' and (resid 353 through 357 or resid 359...FF441 - 44796 - 102
6141TYRTYRTYRTYR(chain 'F' and (resid 353 through 357 or resid 359...FF450105
711CYSCYSLEULEU(chain 'G' and (resid 353 through 357 or resid 359...GG353 - 3578 - 12
721GLUGLUSERSER(chain 'G' and (resid 353 through 357 or resid 359...GG359 - 36214 - 17
731HISHISTYRTYR(chain 'G' and (resid 353 through 357 or resid 359...GG365 - 37320 - 28
741PROPROASPASP(chain 'G' and (resid 353 through 357 or resid 359...GG375 - 37730 - 32
751GLYGLYLEULEU(chain 'G' and (resid 353 through 357 or resid 359...GG382 - 38337 - 38
761ASPASPILEILE(chain 'G' and (resid 353 through 357 or resid 359...GG385 - 39040 - 45
771HISHISVALVAL(chain 'G' and (resid 353 through 357 or resid 359...GG392 - 39947 - 54
781LYSLYSASNASN(chain 'G' and (resid 353 through 357 or resid 359...GG402 - 40557 - 60
791TYRTYRTYRTYR(chain 'G' and (resid 353 through 357 or resid 359...GG40863
7101ASPASPASPASP(chain 'G' and (resid 353 through 357 or resid 359...GG41065
7111GLUGLUVALVAL(chain 'G' and (resid 353 through 357 or resid 359...GG413 - 41868 - 73
7121LEULEUMETMET(chain 'G' and (resid 353 through 357 or resid 359...GG420 - 43875 - 93
7131LYSLYSGLUGLU(chain 'G' and (resid 353 through 357 or resid 359...GG441 - 44796 - 102
7141TYRTYRTYRTYR(chain 'G' and (resid 353 through 357 or resid 359...GG450105
811CYSCYSLEULEU(chain 'H' and (resid 353 through 357 or resid 359...HH353 - 3578 - 12
821GLUGLUSERSER(chain 'H' and (resid 353 through 357 or resid 359...HH359 - 36214 - 17
831HISHISTYRTYR(chain 'H' and (resid 353 through 357 or resid 359...HH365 - 37320 - 28
841PROPROASPASP(chain 'H' and (resid 353 through 357 or resid 359...HH375 - 37730 - 32
851GLYGLYLEULEU(chain 'H' and (resid 353 through 357 or resid 359...HH382 - 38337 - 38
861ASPASPILEILE(chain 'H' and (resid 353 through 357 or resid 359...HH385 - 39040 - 45
871HISHISVALVAL(chain 'H' and (resid 353 through 357 or resid 359...HH392 - 39947 - 54
881LYSLYSASNASN(chain 'H' and (resid 353 through 357 or resid 359...HH402 - 40557 - 60
891TYRTYRTYRTYR(chain 'H' and (resid 353 through 357 or resid 359...HH40863
8101ASPASPASPASP(chain 'H' and (resid 353 through 357 or resid 359...HH41065
8111GLUGLUVALVAL(chain 'H' and (resid 353 through 357 or resid 359...HH413 - 41868 - 73
8121LEULEUMETMET(chain 'H' and (resid 353 through 357 or resid 359...HH420 - 43875 - 93
8131LYSLYSGLUGLU(chain 'H' and (resid 353 through 357 or resid 359...HH441 - 44796 - 102
8141TYRTYRTYRTYR(chain 'H' and (resid 353 through 357 or resid 359...HH450105
112TRPTRPILEILE(chain 'I' and resid 0 through 11)II1 - 112 - 12
212TRPTRPILEILEchain 'K'KK1 - 112 - 12
113TRPTRPALYALY(chain 'J' and resid 0 through 9)JJ1 - 92 - 10
213TRPTRPALYALYchain 'L'LL1 - 92 - 10

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 12829.737 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Protein/peptide
Cyclic peptide 4.2_3


Mass: 1676.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953724980354 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724980354 Å / Relative weight: 1
ReflectionResolution: 2.797→48.01 Å / Num. obs: 27310 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 38.57 Å2 / CC1/2: 0.992 / Net I/σ(I): 6.4
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 3757 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONI

3oni


Resolution: 2.8→42.5 Å / SU ML: 0.4947 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.5455 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3353 1384 5.09 %
Rwork0.2844 25812 -
obs0.287 27196 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.39 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7427 0 0 80 7507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00287652
X-RAY DIFFRACTIONf_angle_d0.65410287
X-RAY DIFFRACTIONf_chiral_restr0.03841034
X-RAY DIFFRACTIONf_plane_restr0.00351319
X-RAY DIFFRACTIONf_dihedral_angle_d13.77544653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.41891320.34542368X-RAY DIFFRACTION90.91
2.9-3.010.37731480.33342568X-RAY DIFFRACTION99.2
3.01-3.150.41471140.3382586X-RAY DIFFRACTION99.23
3.15-3.320.36541650.29352593X-RAY DIFFRACTION99.39
3.32-3.520.30031240.28022593X-RAY DIFFRACTION99.09
3.52-3.80.31391280.27662618X-RAY DIFFRACTION99.31
3.8-4.180.3461470.26322586X-RAY DIFFRACTION99.06
4.18-4.780.31891250.25522616X-RAY DIFFRACTION98.99
4.78-6.020.32771550.28272621X-RAY DIFFRACTION99.21
6.02-42.50.28431460.27182663X-RAY DIFFRACTION97.94
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)
10.4399272108161.10069363776-0.7369663106493.59609425995-2.879431598022.941976528550.175936781522-0.4032981760630.00945652579830.514985148827-0.4028425314170.209533585834-0.00500057657910.195238620730.2049912589070.4242108144440.1007078343060.07244923993721.49427702459-0.08917777333670.3553971994934.640203634976.1667084715460.4703208686
27.10635031352-5.7989632507-0.5723686000377.498614830991.474317047818.98007510010.6905267378780.8927731635470.736226788131-1.0005743477-0.546116071065-0.745913638789-0.04595402324350.766335673827-0.1611680962050.3347423301230.01065573146880.06402481814220.5318169005850.01857214385690.4216605362377.367425781343.314468694741.0764742584
36.1093620805-0.7523641103260.4643541266918.63539321927-1.138584031518.7348031269-0.161249768622-0.463141586837-1.298003956660.4813914432860.1505233910181.235840438690.55913342876-1.886406007450.0273665370810.409445948677-0.101473695090.06058171737320.9195573325520.127483730830.5514219207134.59199029568-7.5846108392156.900452476
42.877383456492.19282654067-1.510813648435.24692381664-1.039604150574.204728115380.0789903950331-1.228362958-0.1306086059950.388985750307-0.340122601236-0.111184329070.03426151926380.8271532346280.2679374978230.2960834424730.02526744795030.09270256433281.005787200040.0211492442210.41508100683714.23865095295.7779274250954.995076471
55.31773624186-1.34851243615-1.518930281052.00197152659-8.153306014057.66651416019-0.0491665373962-0.583848427190.08434686927731.148363479020.6918900921510.0451203485368-0.945270611875-0.602262670588-0.6307664158240.5717317707360.080438592850.02366770455410.967507375519-0.2475955757450.43718882099384.3555733664-33.467120608967.513517856
60.02963492732420.06711928198130.1623402107381.09428692048-0.09593904276051.28374837920.1724978929710.0320396318526-0.0127390414824-0.00855612426572-0.02142206752630.1711809645860.541053810031-0.542203667446-0.1854166114160.5697192282950.0147463887731-0.1302697300351.39914964973-0.1030280484240.34227347584882.5815810736-31.749691143150.6996264317
70.5877880671630.805192715159-0.2532505861532.51381392171-1.344318045366.45783006386-0.03905906816570.622809576552-0.0171332866808-0.564725941304-0.1517266060110.03105824844810.8896789088310.1382567419570.2003668309750.4796044391920.0648608603941-0.02280900782461.33565704837-0.1968780243450.29418642720991.2878122111-32.025813616752.985217395
80.4085059001230.4744891182030.01639927833882.05233849797-0.7749579533554.177089378930.07283837513130.6352629958890.106795318517-0.231382113864-0.2297621096540.2027396884290.03271231891810.09693784011790.1376834620760.337856509719-0.0295270131817-0.01695505082411.36422160922-0.0753043307780.43152545228391.2010655476-22.548521484256.1018305929
91.912068787872.92916548941.321522316676.385947977-0.5879701373834.49660291071-0.05033908764840.1385083814670.413391289171-0.005288536640420.361056920170.05345947714550.269796777233-0.614035390406-0.3241511992620.4673257527590.237192121070.07110033315221.11111765828-0.04484307190210.6029688535652.429733154610.730676670633.2155406456
101.25704873926-1.8162163951-2.201010219444.755413300181.544749132285.10778017698-0.5228891480480.459757375954-0.2542549608520.241151941010.659243715423-0.5876128557460.5148141492081.21555161257-0.09534661320660.2823243228850.03578812432290.1067079199450.6848171474310.02940653809450.57333714731667.72616600139.0637000312946.2969153192
112.005234317794.060811350355.354347421786.440627308322.108019269034.159526521780.114357686896-0.7762078084610.01087197504790.849923258349-0.1556046689660.8541553447160.494292245252-1.147601713320.06827087019210.383890983386-0.04755354611050.1307160984440.879314335899-0.09535645018730.48537560660256.260515032312.780394631347.9347086309
122.110033228210.766257480638-2.086521274251.09437712395-0.2494088164862.378769175370.09004627544250.4339475539740.1653748737040.129260891199-0.1913267069850.6736737145210.278568411094-0.2765025849130.1204209202270.6414620544020.1757522878750.2502542864251.567394252-0.1367489193070.78939100163141.56743285713.496934875447.8361984693
135.509013502413.082518152594.801291728283.732406582550.5348057811226.49768892753-0.0214868479149-0.6938473602040.709350113502-0.08984003713090.1415095910340.411392536595-0.806115231462-0.678960044415-0.1104805241160.4857898522380.1471157027560.06310650835830.459317778477-0.04381545735560.22999848816155.547440563220.077647028343.0196541614
149.778866766331.03499833177-0.1304263640381.223273525911.654601485842.75293292277-0.2908247004490.7973815685590.3814740885-0.4327661620920.289003013119-0.0233626984945-0.392660519311-0.3839042841450.007460747797480.416722129261-0.0868622124350.04770174102620.867567078150.1264378161610.37171180087659.206720835520.059092356833.6763730142
152.000496570283.56022907311-5.677559349632.467243217610.3739624457369.581492113510.1480457203660.2686471178050.3111298555340.2519336416540.2183247004971.81833817612-0.547192706334-1.09374081251-0.3442211002390.510610712251-0.1029811058610.1898561338731.154168193220.19965530241.0355542323742.2724611577-21.31781336336.037613634
161.56197281173-1.001671863752.530790012561.85070042692-1.057257256664.35442205152-0.1620698094070.08122007603220.1103039332520.0153203453415-0.318024617864-0.193035434068-0.1460469615380.38468150270.4584879383120.421735993058-0.00854986599902-0.08998552840421.48726194256-0.07110856616710.38765146520862.4880956232-25.643932861138.8802005245
175.763032394130.4941113887250.7665490726120.884647325894-0.7342502002452.769543776580.0336858034287-0.335041340330.1643206003640.07332606266830.2733594230730.0465457427284-0.1039170217820.00598681239978-0.2743552058880.491661005775-0.03797831004690.03663374587352.02515105989-0.05382706914420.47089476028362.0467978543-17.403995464849.9277292158
180.732779075192-0.195429590335-0.5688319828221.657105537920.7041148987691.336071407630.0546474005633-0.1145927010270.04002812232180.340839731593-0.2065122073950.3402261808830.0123703926224-0.2912260988190.1004800941250.4581543239610.06775914012330.07646665218871.86892306599-0.01902468158010.33743591095450.8054525729-18.675845312644.1813524404
194.79131908589-2.845219313042.99856586558.594023981623.434112606775.815000496540.201492701080.4084724620620.594948276053-1.49682166138-0.355480498401-2.21508840589-0.2874108496731.007258512580.1451890723930.471269482291-0.1426660191840.3239050953481.209390711120.03239202437520.69448424255770.6751378017-14.17125064436.3417765826
202.956253012720.63483770947-1.094958074070.133618210193-0.232150352330.406550006930.2855955415680.6400452518830.339062532031-0.160365991657-0.008234760621910.245650537796-0.315476074682-0.653731556492-0.2581423081290.5937115136480.1621715904920.1270388393241.64629706838-0.0117337086130.40515789908754.1496287425-15.003298295631.9109246704
217.006136943131.66917231755-0.007795802213185.01598998476-1.140483381783.25911207213-0.243758058449-0.0398976483533-0.124108500215-0.6417992175280.145593122634-0.3225805858320.2660899310070.04697119408720.08344434833750.235384018030.01603865665350.110718052824-0.01338804780860.1201663328310.37569848091752.588492103616.3807417069-4.70290521485
224.63438360271-0.106087906754-0.335132897012.161631302620.838746736442.71640060545-0.114894350178-1.356761531-0.3181444793210.33869704469-0.1224608812230.03820052970780.2303962237650.09431294785750.1927608352430.1554686306360.05119229132550.05110865410320.4498914377620.08361190589780.35137233481448.779584388413.03309124648.43822999492
232.671621038151.143359335372.076101342626.204751741111.440628009924.555591285890.1530853778120.05414226306860.112833174277-0.243289476614-0.121418791609-0.0861173848887-0.2320812697560.138629563951-0.07910101553340.08840322087090.1134145342210.09107648928050.0335734525887-0.1661160505660.62265843438644.151677894820.5915528253-2.84342475353
242.318307213974.152771872841.198016976429.419858994185.311981567125.6917718333-0.1683046959640.577305695905-1.02018037847-0.307353128659-0.1676127331181.015304334030.805073761072-0.0434860515710.3640878205120.513239917190.1424066692980.1304726058060.368376925671-0.1137182799071.0668192668151.0983852626-20.7414944005-10.3804763214
252.67857320902-0.4228723725731.109608269893.140707608750.9389952650562.430212839420.161041832465-0.562888538865-0.3532542125780.4693825615260.00817842027523-0.006631539028980.308795304883-0.078451710352-0.1310998453870.264037869213-0.01280363516470.1164115134140.1320792981150.1841596133040.5221036685154.4886885677-11.80562260268.47493475249
261.548106932030.35447963739-0.8192004644723.459308123072.02255740585.947213358620.0206580741446-0.348897962743-0.3868120182670.0008832919853910.08938608528940.06445877910320.643271416739-0.0951862095981-0.03996819097530.262204711502-0.0667139839775-0.06474509747190.1275963727850.04849086633560.48233377771850.9601811141-22.50407261987.72166471308
271.42361230856-1.33256979976-0.6141857389963.246973472460.7645408875482.647207611050.19773491673-0.16828845218-0.292308491740.0962668095997-0.05714810969650.02849873584650.5149320526850.0105196671798-0.09626988742430.1865655490590.02650422113950.1040208446650.0398218018619-0.008808767172660.58807150636245.2414353178-19.62580636163.74216759981
280.8541064541771.011911586410.8258904277811.264214498610.7217965183481.595762176390.162442137480.419561824072-0.0824043906157-0.311050238139-0.1676254229960.03649862546390.006394064951390.02526086478450.0122842419645-0.04933147984210.5753693335420.1564208114080.035120532744-0.02790146778430.6755115376144.4410266873-10.6065257576-2.2221398221
290.526425767467-0.644419131853-0.6435470324991.71262050682-0.00203821831671.447610140730.5415492970170.466998346620.0216286977573-0.381955864026-0.01853561725960.1073295437270.2214381951220.946873693863-0.5371338566550.96707546021-0.172252832449-0.07464950859671.082799021180.1578433667240.4327909574984.3539618804123.937411058624.214797694
300.641882213299-0.582150106620.8792941947482.26083008289-0.0551361916171.51631323138-0.0001703753754160.281122017584-0.03029634219730.05125347616930.05671684832630.0480271774332-0.4619470825890.971953418655-0.05220645565380.272397243068-0.4336208729050.0638950558321.388431011490.06470236511270.488882060496-7.3024584636225.30472621528.86261484133
311.108579752470.584629472681-0.7704626516821.33338339485-1.303210762471.320283332770.000273524582447-0.0453220555991-0.0030718088347-0.2531066939740.120420240518-0.361451574379-0.002291973194360.464680552233-0.1004095390430.564928677485-0.325460293750.08771609226891.95338411457-0.1072862987810.6016687672418.605170458822.341896624712.2781806017
320.67441220390.248907567159-0.255039681690.864333156933-0.0245889622490.327080215754-0.00968086366928-0.154104934810.077815943011-0.1481678027380.118894729065-0.38400739844-0.05954645731270.516501655614-0.1092352146040.670587640514-0.370100648780.01041497809741.82348250667-0.0302688078320.4169742884372.8015101072332.43500705613.9428414711
332.387853771190.7320053834531.50141345612.925958664290.3366439506346.92682658581-0.2901783410850.1564763148870.2174729070820.358421948576-0.0119792095854-0.172164870122-0.3841906751280.2057372232740.2821610096020.861404066207-0.112659765631-0.08440795962791.1506835888-0.04728919109950.28632717814.1717187663833.750304168724.7127039404
344.99158096134-2.09686396818-0.3758442420012.619045908281.102941777740.5408832275490.377842255628-0.9754321616140.07336414951410.255180478326-0.575619120174-0.5003943521330.1173274706870.90719963290.1602539895610.428191383973-0.191365774545-0.03276943702781.112081768940.02122765663830.4152508785059.2698274207-11.35157781422.6257426527
353.220309970410.085796234333-1.022247735011.32780666418-0.5726893942021.047625157220.0989016096263-0.8981010814050.3791396776480.0876695372216-0.228897427071-0.09200570962160.2215801310820.2792219662330.03962553662960.270147471706-0.2279814466440.1480269823790.384901455833-0.1885473278830.5066813241961.63762277051-5.7128026030715.7921412514
364.516187325041.283172761740.5486969579191.67403927922-0.4272478585620.3272544965210.034136253897-0.8383637658090.7309688612270.599751410043-0.07093913201920.586474371872-0.124522201393-0.0271119919180.04040158940410.2754386127790.03275522847180.1022407604030.433037861234-0.1542142686840.386668431475-20.1150438128-5.8413966934916.3445557335
373.225588580881.676564109321.654177164863.423853843111.996453442213.06426223091-0.455986225473-0.01568401802130.2687479977470.2580054874280.009334766328360.2665306706260.2618531764030.1612578492480.4290608040130.5797337923250.135273377785-0.1244687312320.823118975781-0.2866255212820.49158306273957.909244219928.150482395314.5054855482
382.00023644417-5.669328407830.8761406420313.72963156407-1.57727704561.70876751724-0.4249197275660.2517912607360.496331728166-0.3010897225880.278956500493-0.723247239581-0.5064279453530.3077185470860.1384531945110.565110396969-0.1844019497830.1006152373620.600759601108-0.2409901445510.4508214008010.70232363399615.578408373142.517015941
393.19845575431-0.662633585793-2.537135557513.288537816472.870259287035.71493707634-0.00763043008736-0.281214167028-0.0637425502498-0.01888644564260.0644238853960.1328080302510.121749112139-0.198924661029-0.05498710835850.802327463728-0.03061710868950.003985350777951.0392331661-0.07575284838620.2260083558941.238083529413.410597904472.1229556531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 351 through 372 )
2X-RAY DIFFRACTION2chain 'A' and (resid 373 through 395 )
3X-RAY DIFFRACTION3chain 'A' and (resid 396 through 410 )
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 454 )
5X-RAY DIFFRACTION5chain 'B' and (resid 346 through 360 )
6X-RAY DIFFRACTION6chain 'B' and (resid 361 through 410 )
7X-RAY DIFFRACTION7chain 'B' and (resid 411 through 428 )
8X-RAY DIFFRACTION8chain 'B' and (resid 429 through 453 )
9X-RAY DIFFRACTION9chain 'C' and (resid 351 through 372 )
10X-RAY DIFFRACTION10chain 'C' and (resid 373 through 385 )
11X-RAY DIFFRACTION11chain 'C' and (resid 386 through 404 )
12X-RAY DIFFRACTION12chain 'C' and (resid 405 through 410 )
13X-RAY DIFFRACTION13chain 'C' and (resid 411 through 428 )
14X-RAY DIFFRACTION14chain 'C' and (resid 429 through 451 )
15X-RAY DIFFRACTION15chain 'D' and (resid 347 through 360 )
16X-RAY DIFFRACTION16chain 'D' and (resid 361 through 385 )
17X-RAY DIFFRACTION17chain 'D' and (resid 386 through 395 )
18X-RAY DIFFRACTION18chain 'D' and (resid 396 through 428 )
19X-RAY DIFFRACTION19chain 'D' and (resid 429 through 433 )
20X-RAY DIFFRACTION20chain 'D' and (resid 434 through 453 )
21X-RAY DIFFRACTION21chain 'E' and (resid 346 through 372 )
22X-RAY DIFFRACTION22chain 'E' and (resid 373 through 433 )
23X-RAY DIFFRACTION23chain 'E' and (resid 434 through 454 )
24X-RAY DIFFRACTION24chain 'F' and (resid 346 through 360 )
25X-RAY DIFFRACTION25chain 'F' and (resid 361 through 385 )
26X-RAY DIFFRACTION26chain 'F' and (resid 386 through 404 )
27X-RAY DIFFRACTION27chain 'F' and (resid 405 through 433 )
28X-RAY DIFFRACTION28chain 'F' and (resid 434 through 453 )
29X-RAY DIFFRACTION29chain 'G' and (resid 353 through 372 )
30X-RAY DIFFRACTION30chain 'G' and (resid 373 through 395 )
31X-RAY DIFFRACTION31chain 'G' and (resid 396 through 404 )
32X-RAY DIFFRACTION32chain 'G' and (resid 405 through 433 )
33X-RAY DIFFRACTION33chain 'G' and (resid 434 through 454 )
34X-RAY DIFFRACTION34chain 'H' and (resid 346 through 372 )
35X-RAY DIFFRACTION35chain 'H' and (resid 373 through 453 )
36X-RAY DIFFRACTION36chain 'I' and (resid 1 through 12 )
37X-RAY DIFFRACTION37chain 'J' and (resid 1 through 10 )
38X-RAY DIFFRACTION38chain 'K' and (resid 1 through 11 )
39X-RAY DIFFRACTION39chain 'L' and (resid 1 through 8 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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