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- PDB-5o44: Crystal structure of unbranched mixed tri-Ubiquitin chain contain... -

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Basic information

Entry
Database: PDB / ID: 5o44
TitleCrystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages.
Components
  • (Polyubiquitin- ...) x 2
  • Ubiquitin
KeywordsSIGNALING PROTEIN / Mixed linkage Ubiquitin chain
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues ...Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tail fiber / Ubiquitin
Similarity search - Component
Biological speciesMusca domestica (house fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsPadala, P. / Isupov, M.N. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel
CitationJournal: J. Mol. Biol. / Year: 2017
Title: The Crystal Structure and Conformations of an Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.
Authors: Padala, P. / Soudah, N. / Giladi, M. / Haitin, Y. / Isupov, M.N. / Wiener, R.
History
DepositionMay 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
C: Polyubiquitin-B
D: Polyubiquitin-B
B: Polyubiquitin-B
E: Ubiquitin
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,23018
Polymers51,2936
Non-polymers93712
Water68538
1
C: Polyubiquitin-B
D: Polyubiquitin-B
E: Ubiquitin
hetero molecules

C: Polyubiquitin-B
D: Polyubiquitin-B
E: Ubiquitin
hetero molecules

A: Ubiquitin
B: Polyubiquitin-B
F: Polyubiquitin-B
hetero molecules

A: Ubiquitin
B: Polyubiquitin-B
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,46036
Polymers102,58612
Non-polymers1,87524
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
crystal symmetry operation6_445x-y-1,x-1,z+1/61
crystal symmetry operation8_445x-y-1,-y-1,-z1
Buried area22170 Å2
ΔGint-388 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.767, 110.767, 417.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22D
13A
23B
14A
24E
15A
25F
16C
26D
17C
27B
18C
28E
19C
29F
110D
210B
111D
211E
112D
212F
113B
213E
114B
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA1 - 731 - 73
21LEULEUCB1 - 731 - 73
12GLYGLYAA1 - 761 - 76
22GLYGLYDC1 - 761 - 76
13LEULEUAA1 - 731 - 73
23LEULEUBD1 - 731 - 73
14GLYGLYAA1 - 761 - 76
24GLYGLYEE1 - 761 - 76
15GLYGLYAA1 - 761 - 76
25GLYGLYFF1 - 761 - 76
16LEULEUCB1 - 731 - 73
26LEULEUDC1 - 731 - 73
17ARGARGCB1 - 741 - 74
27ARGARGBD1 - 741 - 74
18LEULEUCB1 - 731 - 73
28LEULEUEE1 - 731 - 73
19LEULEUCB1 - 731 - 73
29LEULEUFF1 - 731 - 73
110LEULEUDC1 - 731 - 73
210LEULEUBD1 - 731 - 73
111GLYGLYDC1 - 761 - 76
211GLYGLYEE1 - 761 - 76
112GLYGLYDC1 - 761 - 76
212GLYGLYFF1 - 761 - 76
113LEULEUBD1 - 731 - 73
213LEULEUEE1 - 731 - 73
114LEULEUBD1 - 731 - 73
214LEULEUFF1 - 731 - 73
115GLYGLYEE1 - 761 - 76
215GLYGLYFF1 - 761 - 76

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 2 molecules AE

#1: Protein Ubiquitin


Mass: 8578.809 Da / Num. of mol.: 2 / Mutation: K48C, K63R.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musca domestica (house fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45TR8

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Polyubiquitin- ... , 2 types, 4 molecules CBDF

#2: Protein Polyubiquitin-B


Mass: 8462.727 Da / Num. of mol.: 2 / Mutation: Deleted for Gly 75 and Gly 76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein Polyubiquitin-B


Mass: 8604.845 Da / Num. of mol.: 2 / Mutation: K48R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 3 types, 50 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 7.2 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.3M MgSo4 and 100mM MES monohydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.14→104.25 Å / Num. obs: 27681 / % possible obs: 100 % / Redundancy: 11.4 % / Rsym value: 0.142 / Net I/σ(I): 9.7
Reflection shellResolution: 3.14→3.33 Å / Redundancy: 10 % / Mean I/σ(I) obs: 0.9 / Num. unique all: 4350 / CC1/2: 0.675 / Rsym value: 2.081 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
DMphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B08

3b08


Resolution: 3.14→95.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.25405 1362 4.9 %RANDOM
Rwork0.21691 ---
obs0.21866 26195 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 135.247 Å2
Baniso -1Baniso -2Baniso -3
1-4.72 Å22.36 Å20 Å2
2--4.72 Å20 Å2
3----15.31 Å2
Refinement stepCycle: 1 / Resolution: 3.14→95.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 48 38 3680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193670
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3762.0074940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.12925.181166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.54215734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9561528
X-RAY DIFFRACTIONr_chiral_restr0.1290.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.70513.1151802
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it16.09219.6592242
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it15.54313.6891868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined22.98514363
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43920.1
12C43920.1
21A43860.1
22D43860.1
31A43320.11
32B43320.11
41A44760.11
42E44760.11
51A44260.1
52F44260.1
61C45320.07
62D45320.07
71C46240.1
72B46240.1
81C44320.1
82E44320.1
91C44920.08
92F44920.08
101D44840.09
102B44840.09
111D44660.11
112E44660.11
121D46200.08
122F46200.08
131B43960.11
132E43960.11
141B45000.08
142F45000.08
151E44880.11
152F44880.11
LS refinement shellResolution: 3.14→3.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 90 -
Rwork0.469 1886 -
obs--99.7 %

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