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- PDB-5ohl: K6-specific affimer bound to K6 diUb -

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Basic information

Entry
Database: PDB / ID: 5ohl
TitleK6-specific affimer bound to K6 diUb
Components
  • K6-specific affimer
  • Polyubiquitin-B
KeywordsSIGNALING PROTEIN / ubiquitin / cystatin
Function / homologysymbiont entry into host cell via disruption of host cell glycocalyx / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / symbiont entry into host cell via disruption of host cell envelope / virus tail / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family / Tail fiber
Function and homology information
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMichel, M.A. / Komander, D.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
European Research Council309756 United Kingdom
Medical Research Council (United Kingdom)U105192732 United Kingdom
Lister Institute for Preventive Medicine United Kingdom
European Union283570 United Kingdom
CitationJournal: Mol. Cell / Year: 2017
Title: Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling.
Authors: Michel, M.A. / Swatek, K.N. / Hospenthal, M.K. / Komander, D.
History
DepositionJul 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K6-specific affimer
B: K6-specific affimer
C: K6-specific affimer
D: K6-specific affimer
E: K6-specific affimer
F: K6-specific affimer
G: K6-specific affimer
H: K6-specific affimer
I: Polyubiquitin-B
J: Polyubiquitin-B
K: Polyubiquitin-B
L: Polyubiquitin-B
M: Polyubiquitin-B
N: Polyubiquitin-B
O: Polyubiquitin-B
P: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,60221
Polymers174,39116
Non-polymers6,2115
Water1,892105
1
J: Polyubiquitin-B

A: K6-specific affimer
C: K6-specific affimer
K: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6905
Polymers43,5984
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
MethodPISA
2
A: K6-specific affimer
C: K6-specific affimer
K: Polyubiquitin-B
hetero molecules

J: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)43,6905
Polymers43,5984
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area7480 Å2
ΔGint-45 kcal/mol
Surface area16750 Å2
MethodPISA
3
L: Polyubiquitin-B

B: K6-specific affimer
E: K6-specific affimer
N: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6576
Polymers43,5984
Non-polymers3,0602
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
MethodPISA
4
B: K6-specific affimer
E: K6-specific affimer
N: Polyubiquitin-B
hetero molecules

L: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)46,6576
Polymers43,5984
Non-polymers3,0602
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area7230 Å2
ΔGint-47 kcal/mol
Surface area17360 Å2
MethodPISA
5
I: Polyubiquitin-B

D: K6-specific affimer
H: K6-specific affimer
M: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)43,5984
Polymers43,5984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
MethodPISA
6
D: K6-specific affimer
H: K6-specific affimer
M: Polyubiquitin-B

I: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)43,5984
Polymers43,5984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area7440 Å2
ΔGint-47 kcal/mol
Surface area17090 Å2
MethodPISA
7
F: K6-specific affimer
G: K6-specific affimer
O: Polyubiquitin-B
P: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6576
Polymers43,5984
Non-polymers3,0602
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-42 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.502, 69.672, 99.297
Angle α, β, γ (deg.)79.79, 79.76, 83.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
K6-specific affimer


Mass: 13221.985 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein
Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 8
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C69H140O35 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.5→48.23 Å / Num. obs: 53211 / % possible obs: 98.4 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 0.5 / CC1/2: 0.791 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 4N6U

1ubq

4n6u


Resolution: 2.5→48.23 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.2268 2661 5 %
Rwork0.2001 --
obs0.2015 53198 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10490 0 57 105 10652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510714
X-RAY DIFFRACTIONf_angle_d0.99614391
X-RAY DIFFRACTIONf_dihedral_angle_d16.3614088
X-RAY DIFFRACTIONf_chiral_restr0.041626
X-RAY DIFFRACTIONf_plane_restr0.0041823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54550.36131210.29572627X-RAY DIFFRACTION97
2.5455-2.59440.36391650.28172615X-RAY DIFFRACTION98
2.5944-2.64740.31951200.27932675X-RAY DIFFRACTION98
2.6474-2.70490.37921280.26542656X-RAY DIFFRACTION98
2.7049-2.76790.29991280.25722675X-RAY DIFFRACTION98
2.7679-2.83710.28341430.25612664X-RAY DIFFRACTION99
2.8371-2.91380.28691560.26032639X-RAY DIFFRACTION98
2.9138-2.99950.29911350.24912626X-RAY DIFFRACTION98
2.9995-3.09630.28181370.25172684X-RAY DIFFRACTION99
3.0963-3.20690.28321270.23062708X-RAY DIFFRACTION98
3.2069-3.33530.23761400.22732640X-RAY DIFFRACTION98
3.3353-3.48710.24681290.2092675X-RAY DIFFRACTION98
3.4871-3.67080.24231420.20012668X-RAY DIFFRACTION99
3.6708-3.90070.2581620.19732643X-RAY DIFFRACTION99
3.9007-4.20180.16681480.16712635X-RAY DIFFRACTION99
4.2018-4.62430.15721400.15372708X-RAY DIFFRACTION99
4.6243-5.29270.16621390.15412664X-RAY DIFFRACTION99
5.2927-6.66550.22041340.19172686X-RAY DIFFRACTION99
6.6655-48.24090.17481670.16592649X-RAY DIFFRACTION99

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