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- PDB-5t96: Crystal structure of the infectious salmon anemia virus (ISAV) HE... -

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Basic information

Entry
Database: PDB / ID: 5t96
TitleCrystal structure of the infectious salmon anemia virus (ISAV) HE viral receptor complex
ComponentsHE protein
KeywordsVIRAL PROTEIN / 4-0-acetylsialic acid / hydrolase / hemagglutinin / coiled-coil / viral receptor-complex / infectious salmon anemia virus / ISAV
Function / homologyHaemagglutinin-esterase glycoprotein, infectious salmon anaemia virus-type / Infectious salmon anaemia virus haemagglutinin / metal ion binding / membrane / Chem-79J / FORMIC ACID / HE protein
Function and homology information
Biological speciesInfectious salmon anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsCook, J.D. / Sultana, A. / Lee, J.E.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of the infectious salmon anemia virus receptor complex illustrates a unique binding strategy for attachment.
Authors: Cook, J.D. / Sultana, A. / Lee, J.E.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HE protein
B: HE protein
C: HE protein
D: HE protein
E: HE protein
F: HE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,45154
Polymers225,1716
Non-polymers4,27948
Water29,4371634
1
A: HE protein
B: HE protein
C: HE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,81729
Polymers112,5863
Non-polymers2,23226
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12970 Å2
ΔGint-69 kcal/mol
Surface area36760 Å2
MethodPISA
2
D: HE protein
E: HE protein
F: HE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,63325
Polymers112,5863
Non-polymers2,04822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-54 kcal/mol
Surface area35460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.480, 87.568, 95.534
Angle α, β, γ (deg.)97.140, 113.500, 114.680
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 18:20 or resseq 22:41 or resseq...
21(chain B and (resseq 18:20 or resseq 22:41 or resseq...
31(chain C and (resseq 18:20 or resseq 22:41 or resseq...
41(chain D and (resseq 18:20 or resseq 22:41 or resseq...
51(chain F and (resseq 18:20 or resseq 22:41 or resseq...

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
11LEULEULEULEU(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA18 - 202 - 4
12ASNASNPROPRO(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA22 - 416 - 25
13SERSERPHEPHE(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA43 - 12827 - 112
14GLYGLYGLYGLY(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA130 - 145114 - 129
15SERSERGLYGLY(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA147 - 191131 - 175
16ASNASNSERSER(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA194 - 234178 - 218
17HISHISHISHIS(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA235219
18ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
19ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
110ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
111ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
112ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
113ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
114ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
115ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
116ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
117ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
118ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
119ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
120ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
121ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
122ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
21LEULEULEULEU(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB18 - 202 - 4
22ASNASNPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB22 - 416 - 25
23SERSERPHEPHE(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB43 - 12827 - 112
24GLYGLYGLYGLY(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB130 - 145114 - 129
25SERSERGLYGLY(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB147 - 191131 - 175
26ASNASNSERSER(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB194 - 234178 - 218
27HISHISHISHIS(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB235219
28ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
29ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
210ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
211ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
212ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
213ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
214ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
215ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
216ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
217ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
218ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
219ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
220ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
221ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
222ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
31LEULEULEULEU(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC18 - 202 - 4
32ASNASNPROPRO(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC22 - 416 - 25
33SERSERPHEPHE(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC43 - 12827 - 112
34GLYGLYGLYGLY(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC130 - 145114 - 129
35SERSERGLYGLY(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC147 - 191131 - 175
36ASNASNSERSER(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC194 - 234178 - 218
37HISHISHISHIS(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC235219
38ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
39ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
310ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
311ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
312ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
313ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
314ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
315ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
316ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
317ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
318ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
319ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
320ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
321ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
322ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
41LEULEULEULEU(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD18 - 202 - 4
42ASNASNPROPRO(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD22 - 416 - 25
43SERSERPHEPHE(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD43 - 12827 - 112
44GLYGLYGLYGLY(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD130 - 145114 - 129
45SERSERGLYGLY(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD147 - 191131 - 175
46ASNASNSERSER(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD194 - 234178 - 218
47HISHISHISHIS(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD235219
48ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
49ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
410ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
411ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
412ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
413ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
414ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
415ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
416ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
417ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
418ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
419ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
420ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
421ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
422ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
51LEULEULEULEU(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF18 - 202 - 4
52ASNASNPROPRO(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF22 - 416 - 25
53SERSERPHEPHE(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF43 - 12827 - 112
54GLYGLYGLYGLY(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF130 - 145114 - 129
55SERSERGLYGLY(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF147 - 191131 - 175
56ASNASNSERSER(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF194 - 234178 - 218
57HISHISHISHIS(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF235219
58ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
59ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
510ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
511ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
512ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
513ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
514ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
515ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
516ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
517ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
518ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
519ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
520ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
521ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
522ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
HE protein / Hemagglutinin / Hemagglutinin-esterase glycoprotein


Mass: 37528.578 Da / Num. of mol.: 6 / Fragment: UNP residues 17-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious salmon anemia virus / Gene: HE / Plasmid: pMT-puro / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9J0Y0
#3: Sugar
ChemComp-79J / 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / 4-O-acetyl-5-(acetylamino)-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-D-galacto-non-2-ulosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-galacto-non-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 351.307 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H21NO10

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Non-polymers , 4 types, 1676 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1634 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: [0.2 M] magnesium formate, 20% PEG 3350, w/ a [0.8 M] sodium phosphate, [0.8 M] potassium phosphate, [0.1 M] HEPES pH 7.5 solution as a 1:6 ratio drop additive

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 28, 2016 / Details: 9 CCDS, 9 TILED FIBER-OPTIC TAPERS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→48.4 Å / Num. obs: 138068 / % possible obs: 97.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Net I/σ(I): 14.9 / Num. measured all: 528952
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.033.90.3972603167160.8720.2340.4613.596.6
10.95-48.43.70.02731608440.9990.0160.03238.198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.48 Å48.4 Å
Translation6.48 Å48.4 Å

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.17data scaling
XDSdata reduction
PDB_EXTRACT3.2data extraction
Cootmodel building
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T9Y

5t9y


Resolution: 2→48.396 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 2000 1.45 %Random selection
Rwork0.1385 136056 --
obs0.1391 138056 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.08 Å2 / Biso mean: 37.1833 Å2 / Biso min: 13.23 Å2
Refinement stepCycle: final / Resolution: 2→48.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14631 0 494 1634 16759
Biso mean--49.45 37.67 -
Num. residues----1942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115172
X-RAY DIFFRACTIONf_angle_d1.07220617
X-RAY DIFFRACTIONf_chiral_restr0.0612402
X-RAY DIFFRACTIONf_plane_restr0.0072656
X-RAY DIFFRACTIONf_dihedral_angle_d10.3279003
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8364X-RAY DIFFRACTION4.997TORSIONAL
12B8364X-RAY DIFFRACTION4.997TORSIONAL
13C8364X-RAY DIFFRACTION4.997TORSIONAL
14D8364X-RAY DIFFRACTION4.997TORSIONAL
15F8364X-RAY DIFFRACTION4.997TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.22461440.17969550969497
2.05-2.10540.21921380.16829570970897
2.1054-2.16740.22051420.15279724986697
2.1674-2.23740.22231400.15019623976397
2.2374-2.31730.22111430.14659596973997
2.3173-2.41010.1741350.13939759989498
2.4101-2.51980.1951550.149699985498
2.5198-2.65260.19061410.14089752989398
2.6526-2.81880.20441430.14639714985798
2.8188-3.03640.22171340.14749752988698
3.0364-3.34190.16731470.14379761990899
3.3419-3.82530.17091480.13149848999699
3.8253-4.81880.14431450.11089845999099
4.8188-48.41050.16861450.139698631000899
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)
12.09630.17290.80771.37841.34412.6323-0.02110.0178-0.1789-0.1497-0.0591-0.22180.4334-0.01280.05340.39450.01490.110.14010.0090.295855.0945-0.09233.9983
20.5891-0.1134-0.11530.9682-0.14650.6636-0.00760.1606-0.0148-0.3193-0.0159-0.10760.1691-0.04840.00630.2724-0.00550.0410.1955-0.00160.150545.142818.777-3.0267
30.76180.73540.03925.63863.10264.18060.03230.09-0.2831-0.16640.0513-0.61810.46870.2886-0.19280.38950.09510.14320.23920.01840.442966.3977-1.11754.3788
47.092-5.44746.30274.6135-5.05095.65950.23690.0803-0.1877-0.16940.12040.1284-0.0821-0.0281-0.33920.32070.10110.10510.28510.01570.519377.5418-3.267812.2772
55.4157-1.2544.18227.1764-3.33865.66950.459-0.613-0.87930.2683-0.09-0.24960.57520.4648-0.43630.40120.0945-0.10710.43490.03820.3086106.7749-27.888934.8934
60.8692-0.17480.04431.2954-0.0511.41590.0153-0.0855-0.05560.0182-0.0225-0.12670.171-0.02140.04180.1988-0.0201-0.00560.14210.01970.16647.53956.616730.3254
70.7324-0.17430.24740.822-0.25690.9003-0.0187-0.0672-0.0914-0.00580.02450.04610.2333-0.1837-0.02740.2418-0.06980.0150.2099-0.00240.189334.63334.559823.0218
82.43342.39011.88063.17820.69313.21960.15150.33220.00940.37090.3247-0.25820.26990.1929-0.41810.41120.13530.02260.2258-0.03220.4971.4493-8.173626.9683
92.3674-3.2971.79814.4641-1.78952.0686-0.8323-0.92650.93630.72660.5293-1.2244-0.17160.30660.21690.3870.0445-0.20470.5357-0.11180.6431114.5919-21.766635.9921
101.2283-0.21790.39982.2812-0.36481.4622-0.10540.02620.0078-0.0597-0.0294-0.46470.02220.26620.12590.14920.00330.02580.21070.01830.337467.895423.692716.6222
111.5171-0.46830.27761.0644-0.24030.8106-0.0099-0.02510.04640.04-0.0374-0.1009-0.0565-0.05050.04120.1416-0.0083-0.00480.16950.00030.162649.514529.948222.6412
120.7419-1.74551.32235.3099-2.49753.8089-0.06310.1232-0.1446-0.0441-0.09430.0023-0.20060.06370.19180.1338-0.005-0.02420.2402-0.05170.143634.667934.890720.1931
131.26330.0479-0.02770.8117-0.11670.687-0.025-0.120.08520.0786-0.0405-0.2481-0.04820.05560.0490.156-0.0002-0.03360.172-0.00250.197256.126131.126226.2699
149.0688-6.6003-2.90164.95362.86313.4782-0.1322-0.0432-0.15250.0806-0.1604-0.0490.33590.21020.19960.30970.0740.02130.30430.1240.528580.58965.715926.0067
155.291-6.78614.70359.2761-5.75095.22580.33710.51670.5694-0.1956-0.5226-0.72690.35960.64930.15020.3084-0.0008-0.0840.39380.00090.4622111.3602-23.708227.5397
161.0089-0.2120.14960.87670.34121.395-0.04430.22090.142-0.2091-0.04840.0951-0.2322-0.33180.09580.30110.0077-0.0740.32470.00370.186264.33749.8706-29.938
170.9002-0.40960.00170.80.22911.0467-0.03340.1232-0.0957-0.09120.0007-0.00130.0345-0.08830.04410.197-0.0522-0.01390.2122-0.00090.173575.522437.1222-18.4578
181.3619-0.17650.02840.95850.22271.9639-0.06850.0494-0.2632-0.01630.0686-0.11120.21450.1999-0.01050.1671-0.00590.0020.1633-0.01120.238687.610528.7062-12.1124
190.735-0.16540.06020.60270.18981.6902-0.0730.2539-0.0607-0.1914-0.08510.12830.106-0.41010.09380.2247-0.0736-0.03420.3279-0.03070.22663.257635.9544-26.551
200.95240.250.46590.7606-0.19651.6220.04950.23790.1775-0.2518-0.11060.1343-0.4442-0.51960.13820.34180.0985-0.11140.4979-0.01830.276753.158451.389-28.2724
216.9587-4.83792.04828.1898-4.20933.47730.02740.5791-0.06860.47650.29-0.249-0.6411-0.8846-0.31990.41520.1982-0.07070.7363-0.00230.305843.929459.7115-24.6647
226.6721-3.61611.29955.6303-0.56114.99440.44551.20990.8759-0.7246-0.8151-0.2308-0.11420.78770.2670.53590.08690.05480.64390.23120.506421.505193.6429-33.7047
230.9702-0.2016-0.00891.11120.50230.8710.01310.11010.2119-0.36280.0685-0.1046-0.40630.0542-0.09740.3788-0.06020.04910.19760.02610.207282.759264.8642-17.8113
245.2355-0.30742.41731.54160.41574.0537-0.0612-0.1049-0.0792-0.14250.259-0.2764-0.27470.1511-0.14690.2367-0.09310.08860.2522-0.02280.216599.17150.9891-16.4726
250.8599-0.1595-0.12091.41960.3470.96870.07230.1890.3301-0.440.0459-0.1495-0.4770.0728-0.09250.4816-0.08780.07020.25130.04090.263884.99267.1838-23.2904
265.0916-1.4426-2.17321.26571.20121.6447-0.0001-0.08390.5432-0.2523-0.13770.1479-0.7839-0.57840.15230.79290.307-0.13170.64130.03420.469751.236475.435-23.8261
271.01870.2048-1.12184.03571.25521.8505-0.52430.00851.0630.55190.2403-0.3989-0.2881-0.31890.31470.6260.20360.040.53560.02950.457416.242894.7859-25.2452
280.15490.0308-0.39243.5351-0.86152.6706-0.01590.08190.0196-0.2188-0.03970.24930.0299-0.30360.06030.12620.0085-0.04740.2451-0.0210.219558.21450.7837-1.2353
290.9799-0.1456-0.20410.80780.44270.7959-0.0243-0.05710.00670.04970.0926-0.1239-0.03960.1155-0.07460.1381-0.0169-0.02430.1713-0.00560.157681.432150.81823.4649
300.8675-0.0398-0.4140.64720.23450.79280.0333-0.1003-0.00520.06980.0439-0.086-0.06280.0947-0.06950.1668-0.0026-0.03680.1791-0.01720.183576.836954.07659.4858
312.4606-0.13640.85232.164-1.61063.2786-0.00990.13920.1236-0.16650.12060.2486-0.1868-0.5851-0.17060.23740.1092-0.04820.331-0.04470.294251.473659.9512-2.0425
323.4117-1.49032.5241.9435-2.25582.863-0.0121-0.06460.1734-0.17390.10520.4443-0.4763-0.4214-0.04460.4410.2324-0.11390.5358-0.02750.541744.152268.8381-10.3126
336.3829-6.73197.4227.024-7.77198.5871.06710.5962-0.5802-1.7075-0.53590.6340.91470.533-0.43270.68060.0942-0.04870.4082-0.05960.51217.527384.4605-28.9495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 56 )A17 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 266 )A57 - 266
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 290 )A267 - 290
4X-RAY DIFFRACTION4chain 'A' and (resid 291 through 306 )A291 - 306
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 341 )A307 - 341
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 80 )B17 - 80
7X-RAY DIFFRACTION7chain 'B' and (resid 81 through 290 )B81 - 290
8X-RAY DIFFRACTION8chain 'B' and (resid 291 through 306 )B291 - 306
9X-RAY DIFFRACTION9chain 'B' and (resid 307 through 346 )B307 - 346
10X-RAY DIFFRACTION10chain 'C' and (resid 17 through 52 )C17 - 52
11X-RAY DIFFRACTION11chain 'C' and (resid 53 through 140 )C53 - 140
12X-RAY DIFFRACTION12chain 'C' and (resid 141 through 169 )C141 - 169
13X-RAY DIFFRACTION13chain 'C' and (resid 170 through 290 )C170 - 290
14X-RAY DIFFRACTION14chain 'C' and (resid 291 through 306 )C291 - 306
15X-RAY DIFFRACTION15chain 'C' and (resid 307 through 341 )C307 - 341
16X-RAY DIFFRACTION16chain 'D' and (resid 17 through 56 )D17 - 56
17X-RAY DIFFRACTION17chain 'D' and (resid 57 through 140 )D57 - 140
18X-RAY DIFFRACTION18chain 'D' and (resid 141 through 208 )D141 - 208
19X-RAY DIFFRACTION19chain 'D' and (resid 209 through 266 )D209 - 266
20X-RAY DIFFRACTION20chain 'D' and (resid 267 through 290 )D267 - 290
21X-RAY DIFFRACTION21chain 'D' and (resid 291 through 306 )D291 - 306
22X-RAY DIFFRACTION22chain 'D' and (resid 307 through 337 )D307 - 337
23X-RAY DIFFRACTION23chain 'E' and (resid 17 through 140 )E17 - 140
24X-RAY DIFFRACTION24chain 'E' and (resid 141 through 169 )E141 - 169
25X-RAY DIFFRACTION25chain 'E' and (resid 170 through 290 )E170 - 290
26X-RAY DIFFRACTION26chain 'E' and (resid 291 through 306 )E291 - 306
27X-RAY DIFFRACTION27chain 'E' and (resid 307 through 341 )E307 - 341
28X-RAY DIFFRACTION28chain 'F' and (resid 17 through 56 )F17 - 56
29X-RAY DIFFRACTION29chain 'F' and (resid 57 through 169 )F57 - 169
30X-RAY DIFFRACTION30chain 'F' and (resid 170 through 266 )F170 - 266
31X-RAY DIFFRACTION31chain 'F' and (resid 267 through 290 )F267 - 290
32X-RAY DIFFRACTION32chain 'F' and (resid 291 through 306 )F291 - 306
33X-RAY DIFFRACTION33chain 'F' and (resid 307 through 332 )F307 - 332

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