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- PDB-8adc: Viral tegument-like DUBs -

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Basic information

Entry
Database: PDB / ID: 8adc
TitleViral tegument-like DUBs
ComponentsDeubiquitinating enzyme
KeywordsHYDROLASE / DUBs / deubiquitinating enzymes / ubiquitin / tegument
Function / homologyCathepsin B; Chain A - #120 / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / membrane / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesWaddlia chondrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.7 Å
AuthorsErven, I. / Abraham, E.T. / Hermanns, T. / Baumann, U. / Hofmann, K.
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
Citation
Journal: Nat Commun / Year: 2022
Title: A widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins.
Authors: Erven, I. / Abraham, E. / Hermanns, T. / Baumann, U. / Hofmann, K.
#1: Journal: Nat Commun / Year: 2022
Title: A structural basis for the diverse linkage specificities within the ZUFSP deubiquitinase family.
Authors: Hermanns, T. / Pichlo, C. / Baumann, U. / Hofmann, K.
History
DepositionJul 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_name_com
Item: _entity.pdbx_description
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Deubiquitinating enzyme
A: Deubiquitinating enzyme


Theoretical massNumber of molelcules
Total (without water)48,5632
Polymers48,5632
Non-polymers00
Water2,900161
1
B: Deubiquitinating enzyme


Theoretical massNumber of molelcules
Total (without water)24,2811
Polymers24,2811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Deubiquitinating enzyme


Theoretical massNumber of molelcules
Total (without water)24,2811
Polymers24,2811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.121, 70.295, 75.890
Angle α, β, γ (deg.)90.000, 101.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 284 and (name N or name...
d_2ens_1(chain "B" and ((resid 284 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUALAB1 - 29
d_12ens_1THRTYRB31 - 75
d_13ens_1LEUASPB77 - 106
d_14ens_1PHEARGB108 - 203
d_21ens_1GLUALAA2 - 30
d_22ens_1THRLYSA32 - 70
d_23ens_1THRTYRA74 - 79
d_24ens_1LEUASPA81 - 110
d_25ens_1PHEARGA112 - 207

NCS oper: (Code: givenMatrix: (0.934260764915, 0.00337908583771, 0.356574543285), (0.00444118042566, -0.999987805235, -0.00215992982546), (0.356562896354, 0.00360154957283, -0.934264378955)Vector: -7. ...NCS oper: (Code: given
Matrix: (0.934260764915, 0.00337908583771, 0.356574543285), (0.00444118042566, -0.999987805235, -0.00215992982546), (0.356562896354, 0.00360154957283, -0.934264378955)
Vector: -7.9911063694, 71.0133115014, 36.9943859099)

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Components

#1: Protein Deubiquitinating enzyme / VTD (Viral tegument-like DUB)


Mass: 24281.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Waddlia chondrophila (bacteria) / Strain: ATCC VR-1470 / WSU 86-1044 / Gene: wcw_1294 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: D6YWY5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 38.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium chloride, 0.1 M BisTris pH 5.5, 25 % w/v PEG 3350

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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: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→80 Å / Num. obs: 81659 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1 / Num. unique obs: 13147 / CC1/2: 0.535 / Rrim(I) all: 1.41 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.20_4478refinement
PHENIX1.20_4478refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SIR / Resolution: 1.7→51.06 Å / SU ML: 0.2741 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2351 4045 4.96 %
Rwork0.1975 77461 -
obs0.1993 81506 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→51.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 0 161 3372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073289
X-RAY DIFFRACTIONf_angle_d0.83634453
X-RAY DIFFRACTIONf_chiral_restr0.0497493
X-RAY DIFFRACTIONf_plane_restr0.006588
X-RAY DIFFRACTIONf_dihedral_angle_d10.78551241
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.622424792894 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.44951290.41192602X-RAY DIFFRACTION95.93
1.72-1.740.39141440.37712655X-RAY DIFFRACTION98.56
1.74-1.760.34381500.3562711X-RAY DIFFRACTION98.11
1.76-1.790.36671420.32422611X-RAY DIFFRACTION98.78
1.79-1.810.32271360.31962640X-RAY DIFFRACTION98.09
1.81-1.840.29141110.29282714X-RAY DIFFRACTION98.74
1.84-1.860.30391670.28982652X-RAY DIFFRACTION98.15
1.86-1.890.30731210.2742694X-RAY DIFFRACTION98.74
1.89-1.920.32851410.25512629X-RAY DIFFRACTION98.61
1.92-1.960.2841520.26322672X-RAY DIFFRACTION98.36
1.96-1.990.28141280.23982704X-RAY DIFFRACTION99.26
1.99-2.030.28321270.22542658X-RAY DIFFRACTION98.38
2.03-2.070.22621620.21612633X-RAY DIFFRACTION98.45
2.07-2.120.2541290.20182683X-RAY DIFFRACTION99.4
2.12-2.170.2561310.20132721X-RAY DIFFRACTION98.96
2.17-2.220.22821420.19752671X-RAY DIFFRACTION99.08
2.22-2.280.2751560.1972641X-RAY DIFFRACTION99.04
2.28-2.350.21241310.20662698X-RAY DIFFRACTION98.67
2.35-2.430.25241490.18992684X-RAY DIFFRACTION99.16
2.43-2.510.1961380.19942665X-RAY DIFFRACTION99.12
2.51-2.610.21651440.18582688X-RAY DIFFRACTION98.71
2.61-2.730.28111320.19652641X-RAY DIFFRACTION99.57
2.73-2.880.22461480.18682727X-RAY DIFFRACTION99.48
2.88-3.050.22811440.19092684X-RAY DIFFRACTION99.37
3.06-3.290.25931310.18072683X-RAY DIFFRACTION99.47
3.29-3.620.22981500.17322669X-RAY DIFFRACTION99.16
3.62-4.150.1931390.16272717X-RAY DIFFRACTION99.41
4.15-5.220.16571360.14462647X-RAY DIFFRACTION98.17
5.22-51.060.21691350.2012667X-RAY DIFFRACTION98.73
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)
11.10034929373-1.27675007177-0.04498831676153.52805116057-0.4794288393120.3719917798630.0662940320299-0.06406495291520.12036022115-0.341698028614-0.1165084185120.26931227789-0.065829796421-0.07396784606620.001126253926660.251311829920.00102812251873-0.02626632979590.242797164247-0.005078924005530.267173540238-11.513339041938.716927713334.0248837549
20.4382284390750.7819615079980.2276233605951.980482682650.177666613640.2082080121640.06288107907990.2277243886680.1940416624720.0232609817124-0.00723067161262-1.090696237930.008648819037810.1124049203790.2466006744120.2278181324170.03331158588230.02221773716550.3572008874590.02617947591680.6209621094696.8879418948729.044931537237.9140894531
30.3645615723980.0243103520075-0.3322272888183.568763519030.05043285854870.3182357215730.00893597211982-0.050028128167-0.10028915911-0.144421562861-0.110071841760.0212550752620.092229853404-0.0225254400337-0.008679770096880.1936783096360.0145056784539-0.02462507808520.243968065676-0.02014666025130.222438237662-5.9993536296221.674826343435.9396578513
40.9703132781180.4816436286930.01154891408393.231669061590.8092874095890.6322672727350.2366177774270.128369443389-0.02983329910020.751436944223-0.1114210083780.02678716589380.2151322922640.08663179608520.04237444645590.563993633793-0.03176335651210.05045506317630.2677686940530.003370175816490.2740938750981.9094102559336.15831710382.41445383355
50.9635262977920.1730639115120.1202405568251.440158870390.3117845988370.388524349980.1204765700610.04442026198740.1768185878040.0926684899552-0.012984983836-0.113492534607-0.09279082496680.03972470926111.2489774473E-50.478067632878-0.002380761963940.08458248651180.307818866897-0.00944885236350.2941533315044.0152316364548.000442393-2.15788378105
60.7624824308790.362598365745-0.3329403851251.846497431430.01160664011141.022145086070.0522149941124-0.00661966132704-0.1172727808680.672802980227-0.1124018268550.420496272290.00416850858583-0.1156589692530.1720167617460.6085042320940.00860877575040.1437435937880.313213276779-0.05595945823120.356631192615-1.4136201430650.97133498575.85362147708
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 283 through 351 )BA283 - 3511 - 69
22chain 'B' and (resid 352 through 390)BA352 - 39070 - 104
33chain 'B' and (resid 391 through 493 )BA391 - 493105 - 207
44chain 'A' and (resid 284 through 390 )AB284 - 3901 - 100
55chain 'A' and (resid 391 through 440 )AB391 - 440101 - 150
66chain 'A' and (resid 441 through 493 )AB441 - 493151 - 203

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