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- PDB-5vbt: Crystal structure of a highly specific and potent USP7 ubiquitin ... -

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Basic information

Entry
Database: PDB / ID: 5vbt
TitleCrystal structure of a highly specific and potent USP7 ubiquitin variant inhibitor
ComponentsUBH04
KeywordsDE NOVO PROTEIN / Ubiquitin / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsDONG, A. / DONG, X. / LIU, L. / GUO, Y. / LI, Y. / ZHANG, W. / WALKER, J.R. / SIDHU, S. / Bountra, C. / Arrowsmith, C.H. ...DONG, A. / DONG, X. / LIU, L. / GUO, Y. / LI, Y. / ZHANG, W. / WALKER, J.R. / SIDHU, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of a highly specific and potent USP7 ubiquitin variant inhibitor
Authors: DONG, X. / DONG, A. / LIU, L. / GUO, Y. / LI, Y. / ZHANG, W. / WALKER, J.R. / SIDHU, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
History
DepositionMar 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: UBH04
B: UBH04


Theoretical massNumber of molelcules
Total (without water)17,7532
Polymers17,7532
Non-polymers00
Water2,810156
1
A: UBH04


Theoretical massNumber of molelcules
Total (without water)8,8761
Polymers8,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UBH04


Theoretical massNumber of molelcules
Total (without water)8,8761
Polymers8,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.011, 30.830, 51.046
Angle α, β, γ (deg.)90.000, 97.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UBH04


Mass: 8876.288 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.2 M sodium citrate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 22616 / % possible obs: 98.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.04 / Rrim(I) all: 0.094 / Χ2: 0.899 / Net I/σ(I): 5.9 / Num. measured all: 119284
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.534.50.53511470.7920.2680.6020.51497.4
1.53-1.554.60.4990.8360.250.5610.50197
1.55-1.584.90.4180.8840.2040.4680.51996.9
1.58-1.625.30.3870.8850.1840.4310.54999.9
1.62-1.655.40.380.9190.1760.420.54799.6
1.65-1.695.50.3310.920.1550.3670.54299.8
1.69-1.735.40.2790.9410.1320.310.57599.5
1.73-1.785.30.2340.960.110.260.56199.8
1.78-1.835.10.1970.9740.0940.2190.63298.3
1.83-1.895.10.1620.980.0770.180.66797.5
1.89-1.965.60.140.9860.0650.1550.71699.9
1.96-2.045.60.1160.990.0530.1280.82799.6
2.04-2.135.60.0990.9920.0450.110.91100
2.13-2.245.50.0910.9920.0420.10.97799.6
2.24-2.3850.0870.9930.0420.0971.0697.8
2.38-2.565.70.0780.9940.0350.0861.09699.1
2.56-2.825.70.0740.9940.0330.0811.2499.7
2.82-3.235.40.0640.9950.0290.0711.34499.3
3.23-4.075.10.0580.9950.0270.0641.59497.8
4.07-505.20.0670.9950.0310.0742.33297.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AP4

4ap4


Resolution: 1.51→50.01 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.455 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 1263 5.6 %RANDOM
Rwork0.1598 ---
obs0.1616 21344 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.44 Å2 / Biso mean: 18.028 Å2 / Biso min: 11.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-0.44 Å2
2--1.33 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 1.51→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 0 157 1384
Biso mean---28.79 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191332
X-RAY DIFFRACTIONr_bond_other_d0.0020.021299
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9981816
X-RAY DIFFRACTIONr_angle_other_deg0.94833034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89524.81554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10915255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.986159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211498
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02243
LS refinement shellResolution: 1.505→1.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 90 -
Rwork0.227 1570 -
all-1660 -
obs--96.91 %

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