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- PDB-8cmr: Linear specific OTU-type DUB SnOTU from the pathogen S. negenvens... -

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Basic information

Entry
Database: PDB / ID: 8cmr
TitleLinear specific OTU-type DUB SnOTU from the pathogen S. negenvensis in complex with linear di-ubiquitin
Components
  • OTU domain-containing protein
  • Polyubiquitin-B
KeywordsHYDROLASE / Deubiquitinase / papain-fold / OTU / swapped complex
Function / homology
Function and homology information


Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / OTU domain-containing protein
Similarity search - Component
Biological speciesSimkania negevensis Z (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsUthoff, M. / Hermanns, T. / Boll, V. / Hofmann, K. / Baumann, U.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO 3783/3-1 Germany
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
CitationJournal: Nat Commun / Year: 2023
Title: Functional and structural diversity in deubiquitinases of the Chlamydia-like bacterium Simkania negevensis.
Authors: Boll, V. / Hermanns, T. / Uthoff, M. / Erven, I. / Horner, E.M. / Kozjak-Pavlovic, V. / Baumann, U. / Hofmann, K.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OTU domain-containing protein
B: Polyubiquitin-B
C: OTU domain-containing protein
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)102,0294
Polymers102,0294
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-28 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.618, 154.618, 81.972
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 3 through 242)
d_2ens_1chain "C"
d_1ens_2(chain "B" and (resid 1 through 100 or resid 102 through 152))
d_2ens_2(chain "D" and (resid 1 through 72 or resid 75 through 100 or resid 102 through 152))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LEULEUSERSERAA3 - 2423 - 242
d_21ens_1LEULEUSERSERCC3 - 2423 - 242
d_11ens_2METMETGLUGLUBB1 - 1001 - 100
d_12ens_2VALVALGLYGLYBB102 - 152102 - 152
d_21ens_2METMETARGARGDD1 - 721 - 72
d_22ens_2GLYGLYGLUGLUDD75 - 10075 - 100
d_23ens_2VALVALGLYGLYDD102 - 152102 - 152

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein OTU domain-containing protein


Mass: 33878.930 Da / Num. of mol.: 2 / Mutation: C82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simkania negevensis Z (bacteria) / Gene: SNE_A17630 / Plasmid: popinS / Production host: Escherichia coli (E. coli) / References: UniProt: F8L9T9
#2: Protein Polyubiquitin-B / cDNA FLJ51326 / highly similar to Homo sapiens ubiquitin B (UBB) / mRNA


Mass: 17135.654 Da / Num. of mol.: 2
Fragment: In the crystal structure there is domain swapping likely occurring. The two ubiquitin units of chains B or D are spread over two DUB molecules (A or C). A biological assembly, for example, ...Fragment: In the crystal structure there is domain swapping likely occurring. The two ubiquitin units of chains B or D are spread over two DUB molecules (A or C). A biological assembly, for example, would more likely be Chain A/Chain B:77-152 linked via peptide bond from B152 to D1 to chain D, residues 1-76.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: B4DV12
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: The proteins were purified in 20 mM TRIS pH 7.5, 150 mM NaCl, 2mM DTT and mixed in a 1:1.1 (Protease:ubiquitin) ratio. Reservoir: 0.2 M Magnesium format dihydrate, 20 % w/v PEG 3350, 0.02 M ...Details: The proteins were purified in 20 mM TRIS pH 7.5, 150 mM NaCl, 2mM DTT and mixed in a 1:1.1 (Protease:ubiquitin) ratio. Reservoir: 0.2 M Magnesium format dihydrate, 20 % w/v PEG 3350, 0.02 M EDTA Protein and reservoir were mixed in a ratio of 1 ul : 2 ul.
Temp details: Climate controlled room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→80 Å / Num. obs: 53800 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 57.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.0417 / Rrim(I) all: 0.1406 / Net I/σ(I): 8.9
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.972 / Num. unique obs: 5272 / CC1/2: 0.643 / Rpim(I) all: 0.6039 / Rrim(I) all: 2.072 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XSCALEFeb 5, 2021 BUILT=20210323data scaling
XDSFeb 5, 2021 BUILT=20210323data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2; custom version (https://github.com/muthoff/ComplexFold)

Resolution: 2.24→43.06 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 1339 2.49 %Random (Reflection File Editor, Phenix)
Rwork0.1941 52391 --
obs0.1946 53730 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.88 Å2
Refinement stepCycle: LAST / Resolution: 2.24→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6199 0 0 96 6295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196302
X-RAY DIFFRACTIONf_angle_d0.47168508
X-RAY DIFFRACTIONf_chiral_restr0.0407991
X-RAY DIFFRACTIONf_plane_restr0.00281095
X-RAY DIFFRACTIONf_dihedral_angle_d13.82932426
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.48541777172
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.24634379198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.320.41161350.33955184X-RAY DIFFRACTION99.64
2.32-2.410.29421330.30245203X-RAY DIFFRACTION99.89
2.41-2.520.27541310.27385201X-RAY DIFFRACTION99.96
2.52-2.660.2961320.25715253X-RAY DIFFRACTION99.94
2.66-2.820.29691380.27965233X-RAY DIFFRACTION100
2.82-3.040.26331280.25155196X-RAY DIFFRACTION99.92
3.04-3.350.23231350.24585233X-RAY DIFFRACTION100
3.35-3.830.24321300.20485280X-RAY DIFFRACTION100
3.83-4.820.18841360.14995264X-RAY DIFFRACTION100
4.83-43.060.15491410.13975344X-RAY DIFFRACTION99.84
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)
11.43252645065-0.1467998461440.6313260581560.679495714537-0.1028553597371.22714742197-0.06068296916920.132901654160.04081587163020.047128016946-0.00356278036013-0.0257475209314-0.07156478683390.1876018884410.06564673870110.4590453872390.0103109192290.05146916170580.491620651129-0.01507841530330.525723242284-9.62423082338-55.766690181-2.05682575813
20.395459866086-0.545971733491-0.7828973057940.73645200761.055372748111.48039838356-0.001950774617370.000227365682911-0.1318310639930.0834109289221-0.193514547916-0.03081770061830.105752343434-0.3442477739450.2244383557380.511510498361-0.04579004983180.04035210391180.682880988615-0.07276197472570.57235591979-26.9834014407-61.450651378528.2814771544
31.31843337599-0.4396224931940.4384911979791.25041471269-0.3085626924111.98122672156-0.0675549374202-0.2972019527080.01117951924210.08999660105290.0476522146414-0.03932807341720.0688066497185-0.148478086240.01907123064390.45393773667-0.01820742230590.01448202266030.658942033726-0.09683402188860.509532483703-48.8916274889-32.723142144731.7929574406
41.18422478984-0.302200743967-1.466648535880.2734532780240.827891808112.64020513131-0.0984255088506-0.1634053660080.0383518765030.09680454135480.0114400396968-0.04545941572170.4736114243280.006108619515930.11912673310.628792598904-0.006312827552440.004819375029110.4394449008120.02459880457190.580092543124-44.5837397027-48.90690031070.301350034289
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 2 through 242)AA2 - 2421 - 241
22(chain 'B' and resid 1 through 152)BB1 - 1521 - 150
33(chain 'C' and resid 3 through 242)CC3 - 2421 - 240
44(chain 'D' and resid 1 through 152)DD1 - 1521 - 152

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