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- PDB-5kov: Crystal structure of the human astrovirus 2 capsid protein spike ... -

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Basic information

Entry
Database: PDB / ID: 5kov
TitleCrystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable fragment of an astrovirus neutralizing antibody at 3.24-A resolution
Components
  • Capsid polyprotein VP90
  • PL-2 scFv chain
KeywordsVIRAL PROTEIN / capsid protein / icosahedral virus / single chain variable fragment.
Function / homology
Function and homology information


T=3 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell
Similarity search - Function
Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Capsid polyprotein VP90
Similarity search - Component
Biological speciesHuman astrovirus-2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.245 Å
AuthorsBogdanoff, W.A. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095369 United States
CitationJournal: J. Virol. / Year: 2017
Title: Structure of a Human Astrovirus Capsid-Antibody Complex and Mechanistic Insights into Virus Neutralization.
Authors: Bogdanoff, W.A. / Campos, J. / Perez, E.I. / Yin, L. / Alexander, D.L. / DuBois, R.M.
History
DepositionJul 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid polyprotein VP90
C: PL-2 scFv chain
E: PL-2 scFv chain
B: Capsid polyprotein VP90
H: Capsid polyprotein VP90
K: PL-2 scFv chain
I: PL-2 scFv chain
G: Capsid polyprotein VP90
N: Capsid polyprotein VP90
Q: PL-2 scFv chain
O: PL-2 scFv chain
M: Capsid polyprotein VP90
S: Capsid polyprotein VP90
W: PL-2 scFv chain
U: PL-2 scFv chain
T: Capsid polyprotein VP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)422,55720
Polymers421,67316
Non-polymers8854
Water0
1
A: Capsid polyprotein VP90
C: PL-2 scFv chain
E: PL-2 scFv chain
B: Capsid polyprotein VP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8616
Polymers105,4184
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Capsid polyprotein VP90
K: PL-2 scFv chain
I: PL-2 scFv chain
G: Capsid polyprotein VP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8616
Polymers105,4184
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
N: Capsid polyprotein VP90
Q: PL-2 scFv chain
O: PL-2 scFv chain
M: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)105,4184
Polymers105,4184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
S: Capsid polyprotein VP90
W: PL-2 scFv chain
U: PL-2 scFv chain
T: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)105,4184
Polymers105,4184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.998, 199.998, 157.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 430:447 or resseq 449:473 or resseq...
21(chain B and (resseq 430:447 or resseq 449:473 or resseq...
31(chain G and (resseq 430:447 or resseq 449:473 or resseq...
41(chain H and (resseq 430:447 or resseq 449:473 or resseq...
51(chain M and (resseq 430:447 or resseq 449:473 or resseq...
61(chain N and (resseq 430:447 or resseq 449:473 or resseq...
71(chain S and (resseq 430:447 or resseq 449:473 or resseq...
81(chain T and (resseq 430:447 or resseq 449:473 or resseq...
12(chain E and (resseq 10 or resseq 12:15 or resseq...
22(chain C and (resseq 10 or resseq 12:15 or resseq...
32(chain I and (resseq 10 or resseq 12:15 or resseq...
42(chain K and (resseq 10 or resseq 12:15 or resseq...
52(chain O and (resseq 10 or resseq 12:15 or resseq...
62(chain U and (resseq 10 or resseq 12:15 or resseq...

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
111GLUGLUASPASP(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA430 - 4474 - 21
121GLNGLNASPASP(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA449 - 47323 - 47
131GLYGLYSERSER(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA475 - 49949 - 73
141ASPASPTHRTHR(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA501 - 53175 - 105
151HISHISLYSLYS(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA535 - 598109 - 172
161ASNASNTHRTHR(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA600 - 644174 - 218
211GLUGLUASPASP(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD430 - 4474 - 21
221GLNGLNASPASP(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD449 - 47323 - 47
231GLYGLYSERSER(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD475 - 49949 - 73
241ASPASPTHRTHR(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD501 - 53175 - 105
251HISHISLYSLYS(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD535 - 598109 - 172
261ASNASNTHRTHR(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD600 - 644174 - 218
311GLUGLUASPASP(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH430 - 4474 - 21
321GLNGLNASPASP(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH449 - 47323 - 47
331GLYGLYSERSER(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH475 - 49949 - 73
341ASPASPTHRTHR(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH501 - 53175 - 105
351HISHISLYSLYS(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH535 - 598109 - 172
361ASNASNTHRTHR(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH600 - 644174 - 218
411GLUGLUASPASP(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE430 - 4474 - 21
421GLNGLNASPASP(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE449 - 47323 - 47
431GLYGLYSERSER(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE475 - 49949 - 73
441ASPASPTHRTHR(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE501 - 53175 - 105
451HISHISLYSLYS(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE535 - 598109 - 172
461ASNASNTHRTHR(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE600 - 644174 - 218
511GLUGLUASPASP(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML430 - 4474 - 21
521GLNGLNASPASP(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML449 - 47323 - 47
531GLYGLYSERSER(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML475 - 49949 - 73
541ASPASPTHRTHR(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML501 - 53175 - 105
551HISHISLYSLYS(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML535 - 598109 - 172
561ASNASNTHRTHR(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML600 - 644174 - 218
611GLUGLUASPASP(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI430 - 4474 - 21
621GLNGLNASPASP(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI449 - 47323 - 47
631GLYGLYSERSER(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI475 - 49949 - 73
641ASPASPTHRTHR(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI501 - 53175 - 105
651HISHISLYSLYS(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI535 - 598109 - 172
661ASNASNTHRTHR(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI600 - 644174 - 218
711GLUGLUASPASP(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM430 - 4474 - 21
721GLNGLNASPASP(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM449 - 47323 - 47
731GLYGLYSERSER(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM475 - 49949 - 73
741ASPASPTHRTHR(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM501 - 53175 - 105
751HISHISLYSLYS(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM535 - 598109 - 172
761ASNASNTHRTHR(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM600 - 644174 - 218
811GLUGLUASPASP(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP430 - 4474 - 21
821GLNGLNASPASP(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP449 - 47323 - 47
831GLYGLYSERSER(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP475 - 49949 - 73
841ASPASPTHRTHR(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP501 - 53175 - 105
851HISHISLYSLYS(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP535 - 598109 - 172
861ASNASNTHRTHR(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP600 - 644174 - 218
112GLYGLYGLYGLY(chain E and (resseq 10 or resseq 12:15 or resseq...EC1012
122VALVALSERSER(chain E and (resseq 10 or resseq 12:15 or resseq...EC12 - 1514 - 17
132SERSERPROPRO(chain E and (resseq 10 or resseq 12:15 or resseq...EC17 - 4119 - 43
142GLYGLYPHEPHE(chain E and (resseq 10 or resseq 12:15 or resseq...EC44 - 8046 - 82
152METMETMETMET(chain E and (resseq 10 or resseq 12:15 or resseq...EC8284
162GLYGLYTYRTYR(chain E and (resseq 10 or resseq 12:15 or resseq...EC91 - 9993 - 101
172GLYGLYVALVAL(chain E and (resseq 10 or resseq 12:15 or resseq...EC101 - 113103 - 115
182ASPASPILEILE(chain E and (resseq 10 or resseq 12:15 or resseq...EC1001 - 1002140 - 141
192METMETLEULEU(chain E and (resseq 10 or resseq 12:15 or resseq...EC1004 - 1104143 - 243
1102ILEILEILEILE(chain E and (resseq 10 or resseq 12:15 or resseq...EC1106245
212GLYGLYGLYGLY(chain C and (resseq 10 or resseq 12:15 or resseq...CB1012
222VALVALSERSER(chain C and (resseq 10 or resseq 12:15 or resseq...CB12 - 1514 - 17
232SERSERPROPRO(chain C and (resseq 10 or resseq 12:15 or resseq...CB17 - 4119 - 43
242GLYGLYPHEPHE(chain C and (resseq 10 or resseq 12:15 or resseq...CB44 - 8046 - 82
252METMETMETMET(chain C and (resseq 10 or resseq 12:15 or resseq...CB8284
262GLYGLYTYRTYR(chain C and (resseq 10 or resseq 12:15 or resseq...CB91 - 9993 - 101
272GLYGLYVALVAL(chain C and (resseq 10 or resseq 12:15 or resseq...CB101 - 113103 - 115
282ASPASPILEILE(chain C and (resseq 10 or resseq 12:15 or resseq...CB1001 - 1002140 - 141
292METMETLEULEU(chain C and (resseq 10 or resseq 12:15 or resseq...CB1004 - 1104143 - 243
2102ILEILEILEILE(chain C and (resseq 10 or resseq 12:15 or resseq...CB1106245
312GLYGLYGLYGLY(chain I and (resseq 10 or resseq 12:15 or resseq...IG1012
322VALVALSERSER(chain I and (resseq 10 or resseq 12:15 or resseq...IG12 - 1514 - 17
332SERSERPROPRO(chain I and (resseq 10 or resseq 12:15 or resseq...IG17 - 4119 - 43
342GLYGLYPHEPHE(chain I and (resseq 10 or resseq 12:15 or resseq...IG44 - 8046 - 82
352METMETMETMET(chain I and (resseq 10 or resseq 12:15 or resseq...IG8284
362GLYGLYTYRTYR(chain I and (resseq 10 or resseq 12:15 or resseq...IG91 - 9993 - 101
372GLYGLYVALVAL(chain I and (resseq 10 or resseq 12:15 or resseq...IG101 - 113103 - 115
382ASPASPILEILE(chain I and (resseq 10 or resseq 12:15 or resseq...IG1001 - 1002140 - 141
392METMETLEULEU(chain I and (resseq 10 or resseq 12:15 or resseq...IG1004 - 1104143 - 243
3102ILEILEILEILE(chain I and (resseq 10 or resseq 12:15 or resseq...IG1106245
412GLYGLYGLYGLY(chain K and (resseq 10 or resseq 12:15 or resseq...KF1012
422VALVALSERSER(chain K and (resseq 10 or resseq 12:15 or resseq...KF12 - 1514 - 17
432SERSERPROPRO(chain K and (resseq 10 or resseq 12:15 or resseq...KF17 - 4119 - 43
442GLYGLYPHEPHE(chain K and (resseq 10 or resseq 12:15 or resseq...KF44 - 8046 - 82
452METMETMETMET(chain K and (resseq 10 or resseq 12:15 or resseq...KF8284
462GLYGLYTYRTYR(chain K and (resseq 10 or resseq 12:15 or resseq...KF91 - 9993 - 101
472GLYGLYVALVAL(chain K and (resseq 10 or resseq 12:15 or resseq...KF101 - 113103 - 115
482ASPASPILEILE(chain K and (resseq 10 or resseq 12:15 or resseq...KF1001 - 1002140 - 141
492METMETLEULEU(chain K and (resseq 10 or resseq 12:15 or resseq...KF1004 - 1104143 - 243
4102ILEILEILEILE(chain K and (resseq 10 or resseq 12:15 or resseq...KF1106245
512GLYGLYGLYGLY(chain O and (resseq 10 or resseq 12:15 or resseq...OK1012
522VALVALSERSER(chain O and (resseq 10 or resseq 12:15 or resseq...OK12 - 1514 - 17
532SERSERPROPRO(chain O and (resseq 10 or resseq 12:15 or resseq...OK17 - 4119 - 43
542GLYGLYPHEPHE(chain O and (resseq 10 or resseq 12:15 or resseq...OK44 - 8046 - 82
552METMETMETMET(chain O and (resseq 10 or resseq 12:15 or resseq...OK8284
562GLYGLYTYRTYR(chain O and (resseq 10 or resseq 12:15 or resseq...OK91 - 9993 - 101
572GLYGLYVALVAL(chain O and (resseq 10 or resseq 12:15 or resseq...OK101 - 113103 - 115
582ASPASPILEILE(chain O and (resseq 10 or resseq 12:15 or resseq...OK1001 - 1002140 - 141
592METMETLEULEU(chain O and (resseq 10 or resseq 12:15 or resseq...OK1004 - 1104143 - 243
5102ILEILEILEILE(chain O and (resseq 10 or resseq 12:15 or resseq...OK1106245
612GLYGLYGLYGLY(chain U and (resseq 10 or resseq 12:15 or resseq...UO1012
622VALVALSERSER(chain U and (resseq 10 or resseq 12:15 or resseq...UO12 - 1514 - 17
632SERSERPROPRO(chain U and (resseq 10 or resseq 12:15 or resseq...UO17 - 4119 - 43
642GLYGLYPHEPHE(chain U and (resseq 10 or resseq 12:15 or resseq...UO44 - 8046 - 82
652METMETMETMET(chain U and (resseq 10 or resseq 12:15 or resseq...UO8284
662GLYGLYTYRTYR(chain U and (resseq 10 or resseq 12:15 or resseq...UO91 - 9993 - 101
672GLYGLYVALVAL(chain U and (resseq 10 or resseq 12:15 or resseq...UO101 - 113103 - 115
682ASPASPILEILE(chain U and (resseq 10 or resseq 12:15 or resseq...UO1001 - 1002140 - 141
692METMETLEULEU(chain U and (resseq 10 or resseq 12:15 or resseq...UO1004 - 1104143 - 243
6102ILEILEILEILE(chain U and (resseq 10 or resseq 12:15 or resseq...UO1106245

NCS ensembles :
ID
1
2
DetailsTetramer confirmed by gel filtration

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Components

#1: Protein
Capsid polyprotein VP90


Mass: 25976.566 Da / Num. of mol.: 8 / Fragment: UNP Residues 429-644
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human astrovirus-2 / Gene: ORF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q82446
#2: Antibody
PL-2 scFv chain


Mass: 26732.512 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 cells
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.96 Å3/Da / Density % sol: 68.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Sodium phosphate monobasic.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033029 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033029 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 86484 / % possible obs: 89.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 82.48 Å2 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.092 / Rrim(I) all: 0.185 / Χ2: 7.9 / Net I/av σ(I): 13.31 / Net I/σ(I): 10.6 / Num. measured all: 281483
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.312.50.67476280.6670.4810.8341.72279
3.31-3.452.50.50476780.7220.3680.6282.21279.7
3.45-3.62.40.42478200.8220.310.5282.24481
3.6-3.792.50.37679840.850.2760.4692.31982.7
3.79-4.032.60.27381780.9130.1950.3373.28884.7
4.03-4.342.80.20186180.9460.1350.2435.3889
4.34-4.783.20.17292890.9510.110.2057.49596.2
4.78-5.473.80.17396950.950.1020.2018.38999.8
5.47-6.894.60.1697140.9730.0830.1817.651100
6.89-504.90.1198800.9870.0520.12217.40799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASER6.5.0phasing
PDB_EXTRACT3.2data extraction
Coot0.8.2model building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I30 5KOU

5i30

5kou


Resolution: 3.245→49.999 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 4179 4.84 %
Rwork0.2411 82206 -
obs0.2433 86385 88.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.3 Å2 / Biso mean: 105.7419 Å2 / Biso min: 31.5 Å2
Refinement stepCycle: final / Resolution: 3.245→49.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25887 0 56 0 25943
Biso mean--159.66 --
Num. residues----3263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00426607
X-RAY DIFFRACTIONf_angle_d0.78636180
X-RAY DIFFRACTIONf_chiral_restr0.053991
X-RAY DIFFRACTIONf_plane_restr0.0054590
X-RAY DIFFRACTIONf_dihedral_angle_d10.12915648
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8004X-RAY DIFFRACTION12.854TORSIONAL
12B8004X-RAY DIFFRACTION12.854TORSIONAL
13G8004X-RAY DIFFRACTION12.854TORSIONAL
14H8004X-RAY DIFFRACTION12.854TORSIONAL
15M8004X-RAY DIFFRACTION12.854TORSIONAL
16N8004X-RAY DIFFRACTION12.854TORSIONAL
17S8004X-RAY DIFFRACTION12.854TORSIONAL
18T8004X-RAY DIFFRACTION12.854TORSIONAL
21E5234X-RAY DIFFRACTION12.854TORSIONAL
22C5234X-RAY DIFFRACTION12.854TORSIONAL
23I5234X-RAY DIFFRACTION12.854TORSIONAL
24K5234X-RAY DIFFRACTION12.854TORSIONAL
25O5234X-RAY DIFFRACTION12.854TORSIONAL
26U5234X-RAY DIFFRACTION12.854TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2446-3.28150.3533690.30371616168552
3.2815-3.32010.31851290.33312451258080
3.3201-3.36060.3347990.32682489258879
3.3606-3.40310.41221240.33192421254579
3.4031-3.44790.4261350.30942459259479
3.4479-3.49510.37591250.29572481260680
3.4951-3.5450.34781210.32473259480
3.545-3.59790.34631270.29432481260881
3.5979-3.65410.3861540.282501265581
3.6541-3.7140.29771390.28522531267082
3.714-3.7780.35431280.28112540266882
3.778-3.84670.35161400.29312582272283
3.8467-3.92070.32511360.27262610274684
3.9207-4.00070.33541060.2662619272585
4.0007-4.08760.28431160.2382643275985
4.0876-4.18270.2611740.22982645281986
4.1827-4.28720.24931460.21312742288889
4.2872-4.40310.26381500.20482810296091
4.4031-4.53250.21361360.19962919305593
4.5325-4.67870.27871550.1942990314596
4.6787-4.84580.21691620.18843035319798
4.8458-5.03970.26891560.19833097325399
5.0397-5.26880.24521780.207830933271100
5.2688-5.54620.27471580.195531023260100
5.5462-5.89320.26871550.217531383293100
5.8932-6.34740.30431510.230931133264100
6.3474-6.98470.28511690.246131143283100
6.9847-7.99180.28961380.242631673305100
7.9918-10.05540.22991400.223331693309100
10.0554-50.00540.30061630.27543175333899
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)
10.0021-0.0038-0.0244-0.01950.02140.0251-0.04360.1004-0.06840.0299-0.2555-0.0658-0.22590.056700.4699-0.06810.03820.56820.00860.5052-77.1333-93.613516.8518
20.0482-0.0519-0.04630.10330.02760.02490.0796-0.1898-0.1097-0.0125-0.0850.038-0.76710.1996-00.5375-0.1791-0.05210.437-0.1280.4667-81.571-86.539926.342
30.0083-0.00910.03010.03220.03030.02010.2567-0.21260.0507-0.0874-0.19540.022-0.1347-0.214900.8059-0.1663-0.02510.06180.09290.4646-83.9473-85.729621.3827
40.14770.0285-0.14390.0966-0.1156-0.00260.1170.1548-0.0273-0.0504-0.20850.1381-0.71390.0625-00.6642-0.6206-0.03910.15740.20980.6012-82.0807-87.518711.9603
50.01850.0182-0.01840.0177-0.01660.01240.07780.13650.0311-0.11890.0309-0.0648-0.060.0112-01.1574-0.40950.08320.77570.04210.618-67.1884-80.4461.7498
6-0.04080.1201-0.04080.0108-0.00550.04910.45320.1892-0.14610.2312-0.11110.0524-0.10950.3849-01.1048-1.20580.0791.4605-0.10140.6932-54.5566-83.68341.1857
70.09850.1419-0.0611-0.15-0.0836-0.1262-0.13410.3721-0.212-0.8072-0.14170.1842-0.84541.01520-4.7813-5.43720.0954-3.02520.09990.46-62.9628-89.5654-0.9166
80.0033-0.0004-0.00260.0012-0.00230.00360.0152-0.011-0.0102-0.03020.025-0.07340.0549-0.065400.9918-0.27690.04361.0029-0.05050.81-54.3164-86.212112.3534
90.0699-0.0005-0.03840.10520.00420.03590.1108-0.0404-0.20670.15670.0034-0.0353-0.0218-0.358400.30850.02630.01540.6564-0.10350.5232-112.9631-101.154628.1706
100.00510.0210.0040.0103-0.02830.017-0.1748-0.1011-0.0495-0.0465-0.2104-0.0266-0.0837-0.1008-00.3713-0.0141-0.03790.6157-0.17630.4577-114.1607-105.679523.6365
110.07710.0106-0.01460.05180.00310.05470.0390.1523-0.1055-0.0690.0194-0.0608-0.1137-0.1733-00.4088-0.08180.00540.445-0.00560.6448-104.4547-113.62299.7554
120.01280.01640.02120.00030.02470.00050.0223-0.0550.11610.07250.06190.11910.0096-0.135600.33390.01-0.08250.5010.07080.462-108.9935-117.060311.6781
130.03970.02960.05270.0318-0.02750.03340.02370.00390.0282-0.1371-0.3677-0.13280.09150.0502-01.6478-0.89790.16771.8341-0.22831.0645-49.4645-77.7177-34.6388
140.01510.0085-0.01960.01710.00390.0082-0.0535-0.169-0.0976-0.16310.0620.0942-0.01040.068300.6346-1.02670.03581.4707-0.25080.8058-53.564-89.6448-34.115
150.04180.0040.01560.0004-0.03020.01950.11320.041-0.11770.18730.07750.0051-0.22880.06-01.3567-0.84370.0161.709-0.05440.7939-52.7108-82.372-35.7048
160.02550.01840.0364-0.0092-0.0408-0.0009-0.0531-0.05580.0387-0.0566-0.0649-0.18840.0152-0.40501.1536-0.3649-0.09010.80670.06830.8652-73.6274-81.2846-34.3032
170.0160.1656-0.0472-0.04380.00890.0846-0.3045-0.0175-0.05050.13980.11040.02370.3609-0.317301.109-0.9490.07361.05760.14840.7488-16.7586-40.0483-28.0597
180.0202-0.004-0.02030.0657-0.02350.01330.1910.0790.14480.17790.2272-0.21230.2722-0.3196-01.8707-0.911-0.04481.14850.15270.8589-12.8913-46.8488-31.2948
19-0.02030.0546-0.09910.0561-0.0316-0.0024-0.2712-0.48840.04170.1395-0.1854-0.22630.5814-0.7540-0.4523-2.75350.5268-1.26810.44040.4177-10.681-35.9908-25.2518
200.01030.0470.01410.0426-0.0658-0.0056-0.0970.0312-0.1331-0.032-0.34310.02180.2724-0.18490-0.0685-1.85460.2295-0.02750.15590.5311-10.9666-35.0984-32.164
21-0.00460.0138-0.03090.021-0.02010.0176-0.05980.02010.00610.05820.0058-0.03760.2126-0.0537-00.6419-0.09520.03570.39020.01510.4764-6.0158-25.346-45.1765
220.0477-0.0014-0.0020.0452-0.05180.0514-0.1394-0.09140.0123-0.08880.1894-0.1770.2066-0.8223-00.5356-0.2777-0.0570.5973-0.00730.5536-12.4491-17.1986-51.4183
230.0273-0.00950.0290.0747-0.00980.04230.03-0.12810.0561-0.24710.19470.0063-0.1623-0.1059-00.3383-0.20520.03910.7871-0.04190.554-15.9697-17.8233-52.2172
240.15260.055-0.02440.081-0.08820.021-0.2902-0.14770.04160.08670.0536-0.0160.1176-0.799700.2593-0.47720.1410.7289-0.12920.5681-11.7843-17.3954-40.3403
250.0231-0.0125-0.01720.06470.06470.0326-0.3033-0.0547-0.1394-0.0298-0.1146-0.00610.17070.021602.1896-0.763-0.18151.61620.09490.9315-20.4106-48.49738.2203
26-0.0280.0464-0.02040.0292-0.0070.00750.06740.0395-0.0546-0.10460.1202-0.05920.3631-0.0038-01.6799-1.5689-0.28310.41230.05770.7774-13.4167-49.9146.1437
270.0699-0.0037-0.00260.01870.02890.02590.1507-0.0756-0.01610.17310.046-0.2054-0.0839-0.362601.1215-0.55360.09041.6229-0.1140.8162-16.872-31.07789.2001
28-0.00950.01270.0103-0.0032-0.00020.0183-0.3691-0.023-0.1886-0.02470.0733-0.0315-0.3316-0.118800.8712-0.43780.01291.5408-0.03550.9378-19.8156-27.47295.4205
290.09150.0328-0.01940.0338-0.00310.03180.10720.0005-0.0009-0.18910.0294-0.082-0.54290.021-00.62790.0414-0.08770.3926-0.03030.58821.079813.1585-56.0316
300.03870.0409-0.0486-0.01730.00170.0023-0.0253-0.0753-0.1489-0.1129-0.0796-0.0432-0.22590.0101-00.56380.0126-0.06810.3956-0.02280.3965.672513.8304-50.9246
310.0638-0.030.00490.05910.01570.0544-0.0745-0.25890.12070.1616-0.043-0.1019-0.0951-0.1915-00.4376-0.0613-0.02440.2765-0.04750.52813.48145.8581-37.7016
320.0052-0.0080.0203-0.02310.0799-0.05270.0974-0.0467-0.0051-0.03790.08390.03260.0372-0.09300.4831-0.00640.02950.3392-0.10690.490216.48125.8765-38.8596
330.0092-0.0378-0.01390.05690.02280.02340.58240.06290.22190.0899-0.76770.1634-0.6128-0.4904-00.5789-1.00490.09440.4279-0.17210.8204-58.3474-77.8501-70.9186
340.01530.02110.00670.008-0.0070.00710.2932-0.16470.05460.03340.1347-0.0001-0.099-0.15200.9728-0.31750.05031.0519-0.04090.7567-58.5482-86.7936-69.491
350.07110.02610.06310.0125-0.01180.07910.516-0.373-0.20540.1912-0.4430.1013-0.2520.5927-00.9946-0.6269-0.0340.73240.04410.8519-47.4614-81.8623-72.4225
360.00080.00560.00010.05270.02730.03030.0512-0.2445-0.02650.2428-0.0179-0.02710.1029-0.188701.0672-0.2346-0.09220.64690.05820.7279-54.519-86.6661-74.5734
370.06180.14370.03920.04730.01360.06060.1358-0.0506-0.22920.1254-0.067-0.2012-0.194-0.196100.4637-0.1922-0.01960.5643-0.11380.6451-55.1888-94.3099-97.4887
380.0186-0.0122-0.00860.0324-0.02250.08150.18460.1476-0.07340.0169-0.03160.0088-0.03660.2704-00.5809-0.16160.00510.6598-0.09170.5836-56.65-88.1015-102.5863
390.00740.03390.02340.0174-0.00520.02380.21210.2617-0.16080.03660.1075-0.1783-0.20420.2206-00.5764-0.1345-0.020.4067-0.14870.6797-46.5489-92.6937-95.3837
400.03760.0127-0.01130.04170.03440.0297-0.0440.17320.02020.08920.2434-0.1259-0.0126-0.124100.6507-0.16340.00410.4493-0.04770.6425-52.1056-87.1022-94.2448
410.01440.0324-0.01840.0274-0.03510.03660.0305-0.07-0.21060.3749-0.5613-0.0873-0.1248-0.323601.414-1.64860.18421.6971-0.03160.7568-40.2826-65.0259-44.3501
420.00130.04850.00330.0056-0.00960.01020.01020.0355-0.1677-0.052-0.31610.1154-0.0761-0.0539-01.7719-1.74540.31291.4205-0.07941.0833-35.6132-63.07-49.1627
430.01130.0258-0.0182-0.0080.0410.0110.35720.1027-0.0612-0.1728-0.16410.04820.09620.0617-01.5848-0.6751-0.10751.33330.11350.9432-21.4514-68.2054-60.1542
440.04390.05180.03730.0031-0.0080.03870.164-0.0998-0.0060.18540.08950.22920.13970.036501.3272-1.0027-0.14691.40910.17280.7942-25.0277-62.3057-61.5558
45-0.00190.0008-0.0065-0.00290.00590.0071-0.042-0.0616-0.2106-0.02970.05730.17620.13370.017801.31870.02470.30571.507-0.48331.3072-40.6519-111.4997-118.4558
46-0.00290.0011-0.00950.00770.02010.00650.0259-0.05410.08580.08940.0524-0.1291-0.05760.0727-01.2234-0.31580.25681.658-0.42081.5616-37.4349-104.2532-123.3277
470.0142-0.05340.00220.01740.02080.00430.0145-0.10740.0871-0.1043-0.0542-0.07670.00510.035301.14490.0719-0.00171.4134-0.5331.9848-31.3446-108.8695-110.9363
480.0026-0.0139-0.00370.00110.00270.0010.24030.00670.0059-0.04850.20250.01610.02930.085101.32780.2915-0.26081.1945-0.0881.5868-31.9021-111.8881-98.7298
490.01620.00020.00130.0025-0.0133-0.00240.1898-0.0228-0.0483-0.05930.2649-0.06690.0766-0.0875-00.6166-0.2212-0.0530.6361-0.04350.7256-3.9258-42.1793-95.8111
500.10470.0611-0.06990.05560.09890.0876-0.04620.0644-0.09490.20380.1314-0.19980.0777-0.422500.6635-0.2813-0.17290.41120.03590.6111-8.1449-44.322-84.0092
510.0120.004-0.01-0.0203-0.00320.0178-0.0056-0.03710.01020.17690.1904-0.24320.1069-0.0579-00.7846-0.0609-0.1050.7708-0.04830.9531-5.92-58.9964-93.8349
520.04930.03670.02670.00030.06250.04080.1325-0.004-0.02730.07830.06910.074-0.0454-0.3305-00.5293-0.181-0.08570.4773-0.08810.6298-13.0166-47.4977-88.9999
530.1092-0.0573-0.00060.0281-0.03370.0509-0.75770.25070.2033-0.02830.38430.1006-0.526-0.43200.7258-0.5639-0.09990.93630.10080.7724-21.4463-41.068-114.9042
540.0018-0.00130.00090.0040.00740.0055-0.0452-0.0360.0512-0.0143-0.02830.0089-0.0135-0.02430.00011.10610.15620.00760.9977-0.29321.31111.9288-51.8396-113.7412
550.00440.0404-0.00320.02690.13070.1119-0.47440.18950.0876-0.18840.71280.00420.2658-0.1779-00.7102-0.543-0.03810.9709-0.03090.7541-19.0978-51.3829-112.4924
560.041-0.01420.05220.0112-0.05390.0567-0.16890.0686-0.1304-0.0930.2259-0.1558-0.09830.055700.741-0.34750.04980.9087-0.1020.7219-11.7439-45.5392-112.0509
570.02160.0536-0.01750.0448-0.02280.0419-0.47310.3721-0.00720.00960.0108-0.1748-0.4222-0.3048-01.46-1.5523-0.1151.33940.09410.7595-35.0428-60.297-141.1683
580.05510.00310.00420.0375-0.0240.01880.0246-0.0550.1063-0.17370.0343-0.22750.10160.090801.6488-1.2893-0.07661.8261-0.15771.0105-35.4621-65.5858-138.2927
59-0.00610.11990.00710.003-0.0460.0134-0.1552-0.083-0.01960.19960.6794-0.06910.14720.0501.1834-0.90480.07431.3793-0.11360.8532-34.6501-75.4368-123.8726
60-0.01680.0430.0152-0.00150.01340.0283-0.07470.08080.1253-0.06230.0391-0.0875-0.01410.149101.5264-0.78860.21041.4234-0.17971.0779-38.1849-77.742-127.2353
610.00690.00370.0062-0.0018-0.0039-0.0011-0.07670.06130.0566-0.0169-0.01230.0107-0.03290.0437-01.1239-0.2933-0.46961.65080.33161.665417.0843-62.7081-61.8363
620.0035-0.0092-0.0164-0.00140.00520.0095-0.1828-0.07940.04340.0101-0.1368-0.11960.0643-0.090701.5371-0.0218-0.19771.0150.1391.46447.2599-60.8383-69.0168
630.0234-0.0194-0.03740.0202-0.00530.01120.16990.0561-0.44880.12110.0411-0.0245-0.0048-0.049901.66810.0422-0.27910.97110.04181.76747.3078-66.8618-71.784
640.0004-0.0085-0.0018-0.0018-0.0009-0.00740.13740.0395-0.0538-0.11570.0476-0.050.0920.0115-01.25120.2055-0.21021.3321-0.30521.67226.0745-70.5974-80.9948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 429:456)A429 - 456
2X-RAY DIFFRACTION2(chain A and resid 457:512)A457 - 512
3X-RAY DIFFRACTION3(chain A and resid 513:554)A513 - 554
4X-RAY DIFFRACTION4(chain A and resid 555:644)A555 - 644
5X-RAY DIFFRACTION5(chain B and resid 430:454)B430 - 454
6X-RAY DIFFRACTION6(chain B and resid 455:507)B455 - 507
7X-RAY DIFFRACTION7(chain B and resid 508:637)B508 - 637
8X-RAY DIFFRACTION8(chain B and resid 638:647)B638 - 647
9X-RAY DIFFRACTION9(chain C and resid 1:81)C1 - 81
10X-RAY DIFFRACTION10(chain C and resid 82:115)C82 - 115
11X-RAY DIFFRACTION11(chain C and resid 1001:1073)C1001 - 1073
12X-RAY DIFFRACTION12(chain C and resid 1074:1108)C1074 - 1108
13X-RAY DIFFRACTION13(chain E and resid 1:35)E1 - 35
14X-RAY DIFFRACTION14(chain E and resid 36:69)E36 - 69
15X-RAY DIFFRACTION15(chain E and resid 70:1001)E70 - 1001
16X-RAY DIFFRACTION16(chain E and resid 1002:1107)E1002 - 1107
17X-RAY DIFFRACTION17(chain G and resid 429:497)G429 - 497
18X-RAY DIFFRACTION18(chain G and resid 498:534)G498 - 534
19X-RAY DIFFRACTION19(chain G and resid 535:609)G535 - 609
20X-RAY DIFFRACTION20(chain G and resid 610:647)G610 - 647
21X-RAY DIFFRACTION21(chain H and resid 429:452)H429 - 452
22X-RAY DIFFRACTION22(chain H and resid 453:499)H453 - 499
23X-RAY DIFFRACTION23(chain H and resid 500:549)H500 - 549
24X-RAY DIFFRACTION24(chain H and resid 550:644)H550 - 644
25X-RAY DIFFRACTION25(chain I and resid 1:44)I1 - 44
26X-RAY DIFFRACTION26(chain I and resid 45:98)I45 - 98
27X-RAY DIFFRACTION27(chain I and resid 99:1026)I99 - 1026
28X-RAY DIFFRACTION28(chain I and resid 1027:1108)I1027 - 1108
29X-RAY DIFFRACTION29(chain K and resid 1:82)K1 - 82
30X-RAY DIFFRACTION30(chain K and resid 83:1001)K83 - 1001
31X-RAY DIFFRACTION31(chain K and resid 1002:1054)K1002 - 1054
32X-RAY DIFFRACTION32(chain K and resid 1055:1108)K1055 - 1108
33X-RAY DIFFRACTION33(chain M and resid 429:514)M429 - 514
34X-RAY DIFFRACTION34(chain M and resid 515:544)M515 - 544
35X-RAY DIFFRACTION35(chain M and resid 545:603)M545 - 603
36X-RAY DIFFRACTION36(chain M and resid 604:644)M604 - 644
37X-RAY DIFFRACTION37(chain N and resid 429:499)N429 - 499
38X-RAY DIFFRACTION38(chain N and resid 500:541)N500 - 541
39X-RAY DIFFRACTION39(chain N and resid 542:604)N542 - 604
40X-RAY DIFFRACTION40(chain N and resid 605:645)N605 - 645
41X-RAY DIFFRACTION41(chain O and resid 1:80)O1 - 80
42X-RAY DIFFRACTION42(chain O and resid 81:114)O81 - 114
43X-RAY DIFFRACTION43(chain O and resid 115:1038)O115 - 1038
44X-RAY DIFFRACTION44(chain O and resid 1039:1108)O1039 - 1108
45X-RAY DIFFRACTION45(chain Q and resid 19:51)Q19 - 51
46X-RAY DIFFRACTION46(chain Q and resid 52:78)Q52 - 78
47X-RAY DIFFRACTION47(chain Q and resid 79:1028)Q79 - 1028
48X-RAY DIFFRACTION48(chain Q and resid 1029:1060)Q1029 - 1060
49X-RAY DIFFRACTION49(chain S and resid 429:448)S429 - 448
50X-RAY DIFFRACTION50(chain S and resid 449:548)S449 - 548
51X-RAY DIFFRACTION51(chain S and resid 549:585)S549 - 585
52X-RAY DIFFRACTION52(chain S and resid 586:646)S586 - 646
53X-RAY DIFFRACTION53(chain T and resid 429:529)T429 - 529
54X-RAY DIFFRACTION54(chain T and resid 530:534)T530 - 534
55X-RAY DIFFRACTION55(chain T and resid 535:598)T535 - 598
56X-RAY DIFFRACTION56(chain T and resid 599:644)T599 - 644
57X-RAY DIFFRACTION57(chain U and resid 1:80)U1 - 80
58X-RAY DIFFRACTION58(chain U and resid 81:110)U81 - 110
59X-RAY DIFFRACTION59(chain U and resid 111:1075)U111 - 1075
60X-RAY DIFFRACTION60(chain U and resid 1076:1108)U1076 - 1108
61X-RAY DIFFRACTION61(chain W and resid 5:25)W5 - 25
62X-RAY DIFFRACTION62(chain W and resid 26:55)W26 - 55
63X-RAY DIFFRACTION63(chain W and resid 56:1051)W56 - 1051
64X-RAY DIFFRACTION64(chain W and resid 1052:1097)W1052 - 1097

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