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- PDB-5tla: Crystal structure of mouse ISG15 -

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Basic information

Entry
Database: PDB / ID: 5tla
TitleCrystal structure of mouse ISG15
ComponentsUbiquitin-like protein ISG15
KeywordsSIGNALING PROTEIN / ISG15 / Ub / mouse
Function / homology
Function and homology information


Modulation of host responses by IFN-stimulated genes / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / positive regulation of protein oligomerization / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway ...Modulation of host responses by IFN-stimulated genes / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / positive regulation of protein oligomerization / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / response to bacterium / modification-dependent protein catabolic process / response to virus / protein tag activity / integrin binding / positive regulation of type II interferon production / defense response to virus / defense response to bacterium / extracellular region / cytoplasm
Similarity search - Function
: / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.244 Å
AuthorsGoodwin, O.Y. / Dzimianski, J.V. / Daczkowski, C.M. / Pegan, S.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI109008 United States
United States Department of Agriculture (USDA)58-5030-5-034 United States
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species.
Authors: Daczkowski, C.M. / Dzimianski, J.V. / Clasman, J.R. / Goodwin, O.Y. / Mesecar, A.D. / Pegan, S.D.
History
DepositionOct 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Refinement description / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_audit_support / software
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _pdbx_audit_support.funding_organization / _software.version
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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 / 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: Ubiquitin-like protein ISG15
B: Ubiquitin-like protein ISG15
C: Ubiquitin-like protein ISG15
D: Ubiquitin-like protein ISG15
E: Ubiquitin-like protein ISG15
F: Ubiquitin-like protein ISG15
G: Ubiquitin-like protein ISG15
H: Ubiquitin-like protein ISG15
I: Ubiquitin-like protein ISG15
J: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)169,68510
Polymers169,68510
Non-polymers00
Water00
1
A: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)16,9691
Polymers16,9691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.759, 60.161, 172.658
Angle α, β, γ (deg.)90.000, 93.120, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4:10 or resid 14:18 or resid...
21(chain B and (resid 4:10 or resid 14:18 or resid...
31(chain C and (resid 4:10 or resid 14:18 or resid...
41(chain D and (resid 4:10 or resid 14:18 or resid...
51(chain E and (resid 4:10 or resid 14:18 or resid...
61(chain F and (resid 4:10 or resid 14:18 or resid...
71(chain G and (resid 4:10 or resid 14:18 or resid...
81(chain H and (resid 4:10 or resid 14:18 or resid...
91(chain I and (resid 4:18 or resid 25:43 or resid 45:62 or resid 65:76))
101(chain J and (resid 4:10 or resid 14:18 or resid...
12(chain A and (resid 77:84 or resid 92:111 or resid 117:150))
22(chain B and (resid 77:84 or resid 92:111 or resid 117:150))
32(chain C and (resid 77:84 or resid 92:111 or resid 117:150))
42(chain D and (resid 77:84 or resid 92:111 or resid 117:150))
52(chain E and (resid 77:84 or resid 92:111 or resid 117:150))
62(chain F and (resid 77:84 or resid 92:111 or resid 117:150))
72(chain G and (resid 77:84 or resid 92:111 or resid 117:150))
82(chain H and (resid 77:84 or resid 92:111 or resid 117:150))
92(chain I and (resid 77:84 or resid 92:111 or resid 117:150))
102(chain J and (resid 77:84 or resid 92:150))

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
111ASPASPLEULEU(chain A and (resid 4:10 or resid 14:18 or resid...AA4 - 105 - 11
121ASPASPSERSER(chain A and (resid 4:10 or resid 14:18 or resid...AA14 - 1815 - 19
131VALVALGLNGLN(chain A and (resid 4:10 or resid 14:18 or resid...AA25 - 4326 - 44
141LEULEUGLNGLN(chain A and (resid 4:10 or resid 14:18 or resid...AA45 - 4846 - 49
151LEULEUASPASP(chain A and (resid 4:10 or resid 14:18 or resid...AA52 - 5453 - 55
161LEULEUGLYGLY(chain A and (resid 4:10 or resid 14:18 or resid...AA58 - 6259 - 63
171PROPROSERSER(chain A and (resid 4:10 or resid 14:18 or resid...AA65 - 7666 - 77
211ASPASPLEULEU(chain B and (resid 4:10 or resid 14:18 or resid...BB4 - 105 - 11
221ASPASPSERSER(chain B and (resid 4:10 or resid 14:18 or resid...BB14 - 1815 - 19
231VALVALGLNGLN(chain B and (resid 4:10 or resid 14:18 or resid...BB25 - 4326 - 44
241LEULEUGLNGLN(chain B and (resid 4:10 or resid 14:18 or resid...BB45 - 4846 - 49
251LEULEUASPASP(chain B and (resid 4:10 or resid 14:18 or resid...BB52 - 5453 - 55
261LEULEUGLYGLY(chain B and (resid 4:10 or resid 14:18 or resid...BB58 - 6259 - 63
271PROPROSERSER(chain B and (resid 4:10 or resid 14:18 or resid...BB65 - 7666 - 77
311ASPASPLEULEU(chain C and (resid 4:10 or resid 14:18 or resid...CC4 - 105 - 11
321ASPASPSERSER(chain C and (resid 4:10 or resid 14:18 or resid...CC14 - 1815 - 19
331VALVALGLNGLN(chain C and (resid 4:10 or resid 14:18 or resid...CC25 - 4326 - 44
341LEULEUGLNGLN(chain C and (resid 4:10 or resid 14:18 or resid...CC45 - 4846 - 49
351LEULEUASPASP(chain C and (resid 4:10 or resid 14:18 or resid...CC52 - 5453 - 55
361LEULEUGLYGLY(chain C and (resid 4:10 or resid 14:18 or resid...CC58 - 6259 - 63
371PROPROSERSER(chain C and (resid 4:10 or resid 14:18 or resid...CC65 - 7666 - 77
411ASPASPLEULEU(chain D and (resid 4:10 or resid 14:18 or resid...DD4 - 105 - 11
421ASPASPSERSER(chain D and (resid 4:10 or resid 14:18 or resid...DD14 - 1815 - 19
431VALVALGLNGLN(chain D and (resid 4:10 or resid 14:18 or resid...DD25 - 4326 - 44
441LEULEUGLNGLN(chain D and (resid 4:10 or resid 14:18 or resid...DD45 - 4846 - 49
451LEULEUASPASP(chain D and (resid 4:10 or resid 14:18 or resid...DD52 - 5453 - 55
461LEULEUGLYGLY(chain D and (resid 4:10 or resid 14:18 or resid...DD58 - 6259 - 63
471PROPROSERSER(chain D and (resid 4:10 or resid 14:18 or resid...DD65 - 7666 - 77
511ASPASPLEULEU(chain E and (resid 4:10 or resid 14:18 or resid...EE4 - 105 - 11
521ASPASPSERSER(chain E and (resid 4:10 or resid 14:18 or resid...EE14 - 1815 - 19
531VALVALGLNGLN(chain E and (resid 4:10 or resid 14:18 or resid...EE25 - 4326 - 44
541LEULEUGLNGLN(chain E and (resid 4:10 or resid 14:18 or resid...EE45 - 4846 - 49
551LEULEUASPASP(chain E and (resid 4:10 or resid 14:18 or resid...EE52 - 5453 - 55
561LEULEUGLYGLY(chain E and (resid 4:10 or resid 14:18 or resid...EE58 - 6259 - 63
571PROPROSERSER(chain E and (resid 4:10 or resid 14:18 or resid...EE65 - 7666 - 77
611ASPASPLEULEU(chain F and (resid 4:10 or resid 14:18 or resid...FF4 - 105 - 11
621ASPASPSERSER(chain F and (resid 4:10 or resid 14:18 or resid...FF14 - 1815 - 19
631VALVALGLNGLN(chain F and (resid 4:10 or resid 14:18 or resid...FF25 - 4326 - 44
641LEULEUGLNGLN(chain F and (resid 4:10 or resid 14:18 or resid...FF45 - 4846 - 49
651LEULEUASPASP(chain F and (resid 4:10 or resid 14:18 or resid...FF52 - 5453 - 55
661LEULEUGLYGLY(chain F and (resid 4:10 or resid 14:18 or resid...FF58 - 6259 - 63
671PROPROSERSER(chain F and (resid 4:10 or resid 14:18 or resid...FF65 - 7666 - 77
711ASPASPLEULEU(chain G and (resid 4:10 or resid 14:18 or resid...GG4 - 105 - 11
721ASPASPSERSER(chain G and (resid 4:10 or resid 14:18 or resid...GG14 - 1815 - 19
731VALVALGLNGLN(chain G and (resid 4:10 or resid 14:18 or resid...GG25 - 4326 - 44
741LEULEUGLNGLN(chain G and (resid 4:10 or resid 14:18 or resid...GG45 - 4846 - 49
751LEULEUASPASP(chain G and (resid 4:10 or resid 14:18 or resid...GG52 - 5453 - 55
761LEULEUSERSER(chain G and (resid 4:10 or resid 14:18 or resid...GG58 - 7659 - 77
811ASPASPLEULEU(chain H and (resid 4:10 or resid 14:18 or resid...HH4 - 105 - 11
821ASPASPSERSER(chain H and (resid 4:10 or resid 14:18 or resid...HH14 - 1815 - 19
831VALVALGLNGLN(chain H and (resid 4:10 or resid 14:18 or resid...HH25 - 4826 - 49
841LEULEUASPASP(chain H and (resid 4:10 or resid 14:18 or resid...HH52 - 5453 - 55
851LEULEUGLYGLY(chain H and (resid 4:10 or resid 14:18 or resid...HH58 - 6259 - 63
861PROPROSERSER(chain H and (resid 4:10 or resid 14:18 or resid...HH65 - 7666 - 77
911ASPASPSERSER(chain I and (resid 4:18 or resid 25:43 or resid 45:62 or resid 65:76))II4 - 185 - 19
921VALVALGLNGLN(chain I and (resid 4:18 or resid 25:43 or resid 45:62 or resid 65:76))II25 - 4326 - 44
931LEULEUGLYGLY(chain I and (resid 4:18 or resid 25:43 or resid 45:62 or resid 65:76))II45 - 6246 - 63
941PROPROSERSER(chain I and (resid 4:18 or resid 25:43 or resid 45:62 or resid 65:76))II65 - 7666 - 77
1011ASPASPLEULEU(chain J and (resid 4:10 or resid 14:18 or resid...JJ4 - 105 - 11
1021ASPASPSERSER(chain J and (resid 4:10 or resid 14:18 or resid...JJ14 - 1815 - 19
1031VALVALGLNGLN(chain J and (resid 4:10 or resid 14:18 or resid...JJ25 - 4326 - 44
1041LEULEUGLNGLN(chain J and (resid 4:10 or resid 14:18 or resid...JJ45 - 4846 - 49
1051LEULEUASPASP(chain J and (resid 4:10 or resid 14:18 or resid...JJ52 - 5453 - 55
1061LEULEUGLYGLY(chain J and (resid 4:10 or resid 14:18 or resid...JJ58 - 6259 - 63
1071PROPROSERSER(chain J and (resid 4:10 or resid 14:18 or resid...JJ65 - 7666 - 77
112SERSERVALVAL(chain A and (resid 77:84 or resid 92:111 or resid 117:150))AA77 - 8478 - 85
122ASNASNGLNGLN(chain A and (resid 77:84 or resid 92:111 or resid 117:150))AA92 - 11193 - 112
132GLUGLULEULEU(chain A and (resid 77:84 or resid 92:111 or resid 117:150))AA117 - 150118 - 151
212SERSERVALVAL(chain B and (resid 77:84 or resid 92:111 or resid 117:150))BB77 - 8478 - 85
222ASNASNGLNGLN(chain B and (resid 77:84 or resid 92:111 or resid 117:150))BB92 - 11193 - 112
232GLUGLULEULEU(chain B and (resid 77:84 or resid 92:111 or resid 117:150))BB117 - 150118 - 151
312SERSERVALVAL(chain C and (resid 77:84 or resid 92:111 or resid 117:150))CC77 - 8478 - 85
322ASNASNGLNGLN(chain C and (resid 77:84 or resid 92:111 or resid 117:150))CC92 - 11193 - 112
332GLUGLULEULEU(chain C and (resid 77:84 or resid 92:111 or resid 117:150))CC117 - 150118 - 151
412SERSERVALVAL(chain D and (resid 77:84 or resid 92:111 or resid 117:150))DD77 - 8478 - 85
422ASNASNGLNGLN(chain D and (resid 77:84 or resid 92:111 or resid 117:150))DD92 - 11193 - 112
432GLUGLULEULEU(chain D and (resid 77:84 or resid 92:111 or resid 117:150))DD117 - 150118 - 151
512SERSERVALVAL(chain E and (resid 77:84 or resid 92:111 or resid 117:150))EE77 - 8478 - 85
522ASNASNGLNGLN(chain E and (resid 77:84 or resid 92:111 or resid 117:150))EE92 - 11193 - 112
532GLUGLULEULEU(chain E and (resid 77:84 or resid 92:111 or resid 117:150))EE117 - 150118 - 151
612SERSERVALVAL(chain F and (resid 77:84 or resid 92:111 or resid 117:150))FF77 - 8478 - 85
622ASNASNGLNGLN(chain F and (resid 77:84 or resid 92:111 or resid 117:150))FF92 - 11193 - 112
632GLUGLULEULEU(chain F and (resid 77:84 or resid 92:111 or resid 117:150))FF117 - 150118 - 151
712SERSERVALVAL(chain G and (resid 77:84 or resid 92:111 or resid 117:150))GG77 - 8478 - 85
722ASNASNGLNGLN(chain G and (resid 77:84 or resid 92:111 or resid 117:150))GG92 - 11193 - 112
732GLUGLULEULEU(chain G and (resid 77:84 or resid 92:111 or resid 117:150))GG117 - 150118 - 151
812SERSERVALVAL(chain H and (resid 77:84 or resid 92:111 or resid 117:150))HH77 - 8478 - 85
822ASNASNGLNGLN(chain H and (resid 77:84 or resid 92:111 or resid 117:150))HH92 - 11193 - 112
832GLUGLULEULEU(chain H and (resid 77:84 or resid 92:111 or resid 117:150))HH117 - 150118 - 151
912SERSERVALVAL(chain I and (resid 77:84 or resid 92:111 or resid 117:150))II77 - 8478 - 85
922ASNASNGLNGLN(chain I and (resid 77:84 or resid 92:111 or resid 117:150))II92 - 11193 - 112
932GLUGLULEULEU(chain I and (resid 77:84 or resid 92:111 or resid 117:150))II117 - 150118 - 151
1012SERSERVALVAL(chain J and (resid 77:84 or resid 92:150))JJ77 - 8478 - 85
1022ASNASNLEULEU(chain J and (resid 77:84 or resid 92:150))JJ92 - 15093 - 151

NCS ensembles :
ID
1
2

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Components

#1: Protein
Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein


Mass: 16968.520 Da / Num. of mol.: 10 / Fragment: UNP residues 1-150 / Mutation: C76S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Isg15, G1p2, Ucrp / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64339

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, 12% PEG4000 and 0.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.244→50 Å / Num. obs: 27964 / % possible obs: 98.4 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.052 / Net I/av σ(I): 17.371 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.25-3.312.10.3750.77188
3.31-3.372.30.380.841198.9
3.37-3.432.30.3610.89198.2
3.43-3.52.30.2690.938197.8
3.5-3.582.40.3260.909198.9
3.58-3.662.40.3070.914198.9
3.66-3.752.40.1810.932198.5
3.75-3.852.40.1920.964199
3.85-3.972.40.1410.966198.3
3.97-4.092.40.10.987198.8
4.09-4.242.40.0780.992199.1
4.24-4.412.40.0580.995199.1
4.41-4.612.40.0520.996199.3
4.61-4.852.40.050.996199.4
4.85-5.162.40.0410.997199.5
5.16-5.562.40.0440.996199.3
5.56-6.112.40.0460.996199.4
6.11-72.40.040.997199.4
7-8.812.40.0210.999199.2
8.81-502.30.0120.999198.4

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Processing

Software
NameVersionClassification
PHENIXdev_2420refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JZE

5jze


Resolution: 3.244→42.183 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3091 1396 5 %
Rwork0.2563 26533 -
obs0.2589 27929 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 272.01 Å2 / Biso mean: 115.8566 Å2 / Biso min: 46.44 Å2
Refinement stepCycle: final / Resolution: 3.244→42.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11491 0 0 0 11491
Num. residues----1457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211671
X-RAY DIFFRACTIONf_angle_d0.56715746
X-RAY DIFFRACTIONf_chiral_restr0.0431843
X-RAY DIFFRACTIONf_plane_restr0.0041992
X-RAY DIFFRACTIONf_dihedral_angle_d12.5957123
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2448X-RAY DIFFRACTION9.759TORSIONAL
12B2448X-RAY DIFFRACTION9.759TORSIONAL
13C2448X-RAY DIFFRACTION9.759TORSIONAL
14D2448X-RAY DIFFRACTION9.759TORSIONAL
15E2448X-RAY DIFFRACTION9.759TORSIONAL
16F2448X-RAY DIFFRACTION9.759TORSIONAL
17G2448X-RAY DIFFRACTION9.759TORSIONAL
18H2448X-RAY DIFFRACTION9.759TORSIONAL
19I2448X-RAY DIFFRACTION9.759TORSIONAL
110J2448X-RAY DIFFRACTION9.759TORSIONAL
21A3100X-RAY DIFFRACTION9.759TORSIONAL
22B3100X-RAY DIFFRACTION9.759TORSIONAL
23C3100X-RAY DIFFRACTION9.759TORSIONAL
24D3100X-RAY DIFFRACTION9.759TORSIONAL
25E3100X-RAY DIFFRACTION9.759TORSIONAL
26F3100X-RAY DIFFRACTION9.759TORSIONAL
27G3100X-RAY DIFFRACTION9.759TORSIONAL
28H3100X-RAY DIFFRACTION9.759TORSIONAL
29I3100X-RAY DIFFRACTION9.759TORSIONAL
210J3100X-RAY DIFFRACTION9.759TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2439-3.35980.37411370.34382517265494
3.3598-3.49430.39921290.3292612274198
3.4943-3.65320.4581380.33442608274699
3.6532-3.84570.39351500.33232640279099
3.8457-4.08650.341330.26862656278999
4.0865-4.40170.3141480.23722629277799
4.4017-4.84410.30111390.22222670280999
4.8441-5.54370.27911490.22122709285899
5.5437-6.97930.32851190.27972724284399
6.9793-42.18610.23571540.22072768292299
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)
15.29370.10332.27280.9226-0.03394.30650.00590.30780.4912-0.0405-0.0475-0.24630.1350.35830.00130.70420.18490.12530.54630.12420.617334.274726.82760.7066
23.734-0.39770.25635.34750.54011.6396-0.3118-0.39040.57690.18260.35430.41520.13840.2491-0.00040.70240.1553-0.04480.6542-0.02790.692219.42742.831867.9989
32.0205-1.24870.14512.4870.97415.49310.42160.1774-0.4019-0.14660.16860.07380.38580.54330.00160.57070.11640.02390.75280.01990.53751.025415.236370.7054
46.6759-1.0985-1.90132.8020.01233.46880.008-0.4995-0.5171-0.2932-0.01380.77640.1753-0.07380.00020.72050.1382-0.20540.57090.07330.8593-2.621548.315466.8642
54.7256-1.8245-0.16725.6347-2.22032.1036-0.37460.17140.1503-0.29830.0409-0.74140.15850.0820.0010.58160.0527-0.0440.7691-0.04430.721369.61784.103163.1635
63.2481.77870.27272.6763-0.63653.7763-0.10610.08150.61820.33650.17370.1876-0.32240.3485-0.00111.033-0.10830.17640.8085-0.01771.139437.2534.455626.6698
75.34073.9625-0.55913.5602-0.17923.6089-0.28690.5995-0.2808-0.5050.1597-0.95340.1514-0.1538-0.00140.937-0.00760.2210.77570.0781.115322.438519.302621.9426
85.50891.0453.0273.45940.65951.6424-0.73610.65041.4792-0.30980.30980.1706-0.01191.1408-0.03640.7767-0.24870.05681.28710.21690.923555.353543.80419.008
93.63911.2189-0.20394.30681.94531.6439-0.309-0.06140.205-1.02920.28571.0899-0.1049-0.2251-0.00230.8669-0.1903-0.1310.83840.34931.7110.860712.262423.9435
101.8886-0.44771.45052.5591-0.07630.6335-0.85670.4351.1952-0.34460.51270.14390.09160.9214-0.00641.1169-0.218-0.14431.38330.25551.456374.787952.626727.9083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:150)A0 - 150
2X-RAY DIFFRACTION2(chain B and resid 0:150)B0 - 150
3X-RAY DIFFRACTION3(chain C and resid 1:150)C1 - 150
4X-RAY DIFFRACTION4(chain D and resid 3:150)D3 - 150
5X-RAY DIFFRACTION5(chain E and resid 1:150)E1 - 150
6X-RAY DIFFRACTION6(chain F and resid 0:150)F0 - 150
7X-RAY DIFFRACTION7(chain G and resid 2:150)G2 - 150
8X-RAY DIFFRACTION8(chain H and resid 3:150)H3 - 150
9X-RAY DIFFRACTION9(chain I and resid 3:150)I3 - 150
10X-RAY DIFFRACTION10(chain J and resid 0:150)J0 - 150

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