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- PDB-5o6s: UbV.B4R, a dimeric ubiquitin variant binding to BIRC4 RING -

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Basic information

Entry
Database: PDB / ID: 5o6s
TitleUbV.B4R, a dimeric ubiquitin variant binding to BIRC4 RING
ComponentsPolyubiquitin-B
KeywordsPROTEIN BINDING / Ubiquitin variant
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGabrielsen, M. / Buetow, L. / Huang, D.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC596/A23278 United Kingdom
European Research Council647849 United Kingdom
CitationJournal: Mol. Cell / Year: 2017
Title: A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants.
Authors: Gabrielsen, M. / Buetow, L. / Nakasone, M.A. / Ahmed, S.F. / Sibbet, G.J. / Smith, B.O. / Zhang, W. / Sidhu, S.S. / Huang, D.T.
History
DepositionJun 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Polyubiquitin-B
B: Polyubiquitin-B
C: Polyubiquitin-B
D: Polyubiquitin-B
E: Polyubiquitin-B
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)55,4556
Polymers55,4556
Non-polymers00
Water55831
1
A: Polyubiquitin-B
B: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)18,4852
Polymers18,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-23 kcal/mol
Surface area9040 Å2
MethodPISA
2
C: Polyubiquitin-B
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)18,4852
Polymers18,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-24 kcal/mol
Surface area8960 Å2
MethodPISA
3
E: Polyubiquitin-B
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)18,4852
Polymers18,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-25 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.213, 71.669, 118.033
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Polyubiquitin-B


Mass: 9242.483 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Variant of ubiquitin identified from phage-display / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pGEX4T.1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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 Å3/Da / Density % sol: 38.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: (0.2 M Zinc acetate, 0.1 M phosphate-citrate pH 4.2, 40 % PEG 300

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→58.79 Å / Num. obs: 8941 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 58.4 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.167 / Net I/σ(I): 3.7
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.523 / Num. unique obs: 1423 / CC1/2: 0.725 / Rpim(I) all: 0.513 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 2.9→58.79 Å / Cor.coef. Fo:Fc: 0.833 / Cor.coef. Fo:Fc free: 0.785 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.551
RfactorNum. reflection% reflectionSelection details
Rfree0.309 483 5.41 %RANDOM
Rwork0.261 ---
obs0.263 8936 99.3 %-
Displacement parametersBiso mean: 58.27 Å2
Baniso -1Baniso -2Baniso -3
1--10.2656 Å20 Å219.9501 Å2
2--12.6067 Å20 Å2
3----2.3411 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: 1 / Resolution: 2.9→58.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 0 32 3524
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083619HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064871HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1359SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes487HARMONIC5
X-RAY DIFFRACTIONt_it3619HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.78
X-RAY DIFFRACTIONt_other_torsion21.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion505SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3860SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.35 138 5.41 %
Rwork0.255 2413 -
all0.261 2551 -
obs--99.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.00171.99941.56571.50013.44574.09470.0401-0.1338-0.18360.17030.1771-0.01250.17670.2733-0.2172-0.04380.0488-0.1514-0.12180.0562-0.0161-22.236137.0449-23.4807
2-0.15231.89910.75983.78122.59413.4516-0.03070.1182-0.230.4642-0.00730.11930.0589-0.07140.038-0.08850.0034-0.0169-0.07910.0397-0.0022-44.569829.3498-30.7247
32.49712.83680.5955.20461.24311.1635-0.05010.01170.08430.02990.1075-0.0549-0.02240.0909-0.0573-0.20230.0422-0.05640.0460.0262-0.1582-13.227428.29741.0739
42.7980.61680.32642.2540.64021.4836-0.0182-0.0338-0.04920.3395-0.0920.1649-0.0488-0.36630.1103-0.04130.0161-0.0427-0.11330.0033-0.2503-32.430311.53736.8108
52.3836-1.6183-0.39784.10163.35512.0632-0.0048-0.21930.257-0.00450.03030.0144-0.0354-0.2044-0.02550.02440.0293-0.2281-0.2822-0.05050.04076.128145.5871-20.7895
61.83950.3207-0.30173.40483.76285.67380.04330.1283-0.05150.01110.1073-0.448-0.05170.0263-0.1506-0.05710.0092-0.1125-0.09390.0592-0.170620.002536.8391-40.2495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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