[English] 日本語
Yorodumi
- PDB-5kov: Crystal structure of the human astrovirus 2 capsid protein spike ... -

+
Open data


ID or keywords:

Loading...

-
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 / host extracellular space
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
Revision 1.8Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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


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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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: _

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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more