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- PDB-7pl7: Crystal structure of yeast Otu2 OTU domain -

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Basic information

Entry
Database: PDB / ID: 7pl7
TitleCrystal structure of yeast Otu2 OTU domain
ComponentsOTU domain-containing protein 2
KeywordsHYDROLASE / deubiquitination / translation / 40S ribosomal subunit
Function / homology
Function and homology information


protein deubiquitination / cysteine-type deubiquitinase activity / cytoplasm
Similarity search - Function
: / : / OTU-like cysteine protease / OTU domain / OTU domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
OTU domain-containing protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsIvic, N. / Cheng, J. / Becker, T. / Ikeuchi, K.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB/TRR-174 Germany
German Research Foundation (DFG)BE1814/15-1 Germany
German Research Foundation (DFG)BE1814/1-1 Germany
CitationJournal: To Be Published
Title: Crystal structure of yeast Otu2 OTU domain
Authors: Ikeuchi, K.
History
DepositionAug 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OTU domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)19,4491
Polymers19,4491
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.669, 60.055, 148.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

#1: Protein OTU domain-containing protein 2


Mass: 19449.162 Da / Num. of mol.: 1 / Mutation: C178S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OTU2, YHL013C / Production host: Escherichia coli (E. coli) / References: UniProt: P38747
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M KSCN 0.1 M BisTris propane pH 6.5 20% PEG 3350 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 16, 2020 / Details: Si(111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→42.772 Å / Num. obs: 11976 / % possible obs: 99.8 % / Redundancy: 7.091 % / Biso Wilson estimate: 62.783 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.142 / Χ2: 0.808 / Net I/σ(I): 13.95 / Num. measured all: 84923
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.59-2.757.1971.0022.3513854195419250.8981.0898.5
2.75-2.947.2320.6743.9312923178717870.9560.726100
2.94-3.176.8830.4436.5611757170817080.9770.48100
3.17-3.477.1050.27711.3411113156415640.9920.298100
3.47-3.887.3160.16617.1610162138913890.9950.179100
3.88-4.476.9380.09524.258707125512550.9970.103100
4.47-5.466.8680.07328.167301106310630.9960.08100
5.46-7.667.280.06929.3559268148140.9980.074100
7.66-42.7726.7460.04339.3231644724690.9990.04799.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BOU

4bou


Resolution: 2.6→42.772 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 321 4.98 %
Rwork0.2252 6124 -
obs0.2271 6445 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.99 Å2 / Biso mean: 74.6578 Å2 / Biso min: 31.24 Å2
Refinement stepCycle: final / Resolution: 2.6→42.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 27 1308
Biso mean---67.58 -
Num. residues----155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6001-3.27570.32181560.2632987
3.2757-42.7720.24781650.21443137
Refinement TLS params.Method: refined / Origin x: 10.4451 Å / Origin y: 31.7461 Å / Origin z: 56.3871 Å
111213212223313233
T0.3562 Å20.0743 Å2-0.0269 Å2-0.3425 Å2-0.0395 Å2--0.4603 Å2
L3.2086 °2-0.5789 °2-0.0527 °2-2.9988 °2-0.9976 °2--6.182 °2
S-0.1982 Å °-0.3181 Å °0.21 Å °0.2364 Å °0.1079 Å °-0.3521 Å °-0.4167 Å °0.2738 Å °0.0651 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 148 through 307)

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