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

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Basic information

Entry
Database: PDB / ID: 8add
TitleViral tegument-like DUBs
ComponentsATP-dependent DNA helicase
KeywordsHYDROLASE / deubiquitinating enzyme / ubiquitin / tegument
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / DNA helicase / DNA recombination / hydrolase activity / DNA repair / ATP binding
Similarity search - Function
Helitron helicase-like domain / Domain of unknown function DUF6570 / Helitron helicase-like domain at N-terminus / Domain of unknown function (DUF6570) / : / DNA helicase Pif1, 2B domain / : / DNA helicase Pif1-like / PIF1-like helicase / Herpesvirus large tegument protein, USP domain ...Helitron helicase-like domain / Domain of unknown function DUF6570 / Helitron helicase-like domain at N-terminus / Domain of unknown function (DUF6570) / : / DNA helicase Pif1, 2B domain / : / DNA helicase Pif1-like / PIF1-like helicase / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Papain-like cysteine peptidase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent DNA helicase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.9 Å
AuthorsErven, I. / Abraham, E.T. / Hermanns, T. / 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
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.
#2: Journal: Nat Commun / Year: 2018
Title: A family of unconventional deubiquitinases with modular chain specificity determinants.
Authors: Hermanns, T. / Pichlo, C. / Woiwode, I. / Klopffleisch, K. / Witting, K.F. / Ovaa, H. / Baumann, U. / Hofmann, K.
History
DepositionJul 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 2.0Sep 4, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1Nov 6, 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
A: ATP-dependent DNA helicase


Theoretical massNumber of molelcules
Total (without water)24,0031
Polymers24,0031
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.010, 120.670, 34.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein ATP-dependent DNA helicase


Mass: 24002.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: LOC101884770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8M9QCC7, DNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 20% w/v PEG 6000

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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: 0.9747 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 37456 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 23.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.172 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 2724 / CC1/2: 0.621 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4478refinement
PHENIX1.20_4478refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SIR / Resolution: 1.9→42.37 Å / SU ML: 0.1445 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 2783 7.43 %
Rwork0.162 34656 -
obs0.1655 37439 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 0 158 1824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491705
X-RAY DIFFRACTIONf_angle_d0.84842302
X-RAY DIFFRACTIONf_chiral_restr0.0449257
X-RAY DIFFRACTIONf_plane_restr0.0063302
X-RAY DIFFRACTIONf_dihedral_angle_d6.5956231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.3471380.27541695X-RAY DIFFRACTION99.84
1.93-1.970.23341400.2351722X-RAY DIFFRACTION100
1.97-2.010.251490.20421744X-RAY DIFFRACTION100
2.01-2.050.25441280.20171723X-RAY DIFFRACTION100
2.05-2.090.21731430.17371734X-RAY DIFFRACTION99.89
2.09-2.140.24181380.15841767X-RAY DIFFRACTION100
2.14-2.190.21931390.1561670X-RAY DIFFRACTION100
2.19-2.250.21051380.16451768X-RAY DIFFRACTION100
2.25-2.320.18831390.15451726X-RAY DIFFRACTION100
2.32-2.390.18011470.15861726X-RAY DIFFRACTION100
2.39-2.480.22211320.15221773X-RAY DIFFRACTION100
2.48-2.580.21321330.16271714X-RAY DIFFRACTION100
2.58-2.70.20551400.15941732X-RAY DIFFRACTION100
2.7-2.840.18831380.1671759X-RAY DIFFRACTION100
2.84-3.020.20621450.16121713X-RAY DIFFRACTION100
3.02-3.250.21041480.16121741X-RAY DIFFRACTION100
3.25-3.580.19051420.15041713X-RAY DIFFRACTION100
3.58-4.090.18041290.14371737X-RAY DIFFRACTION100
4.09-5.150.1821400.13121753X-RAY DIFFRACTION100
5.16-42.370.27861370.18331746X-RAY DIFFRACTION99.89
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)
10.533327544469-0.237877795855-0.0125560173010.356681099192-0.4743777949590.9603272337642.23052499265E-50.01416635291280.037201915930.109843926265-0.09842153570160.04588210469540.0921291420512-0.0961815769008-0.001131356055330.1639723360850.002620656385210.007244330346170.159570251912-0.01893917494770.18319074945436.019384528610.747549367428.6155650616
20.233282683514-0.02795750463860.03784760981250.158925562416-0.02524508354660.19202883679-0.0865520802440.265631011640.0865235186401-0.07267417742790.07502581372280.1622845076050.155968619394-0.298333499003-0.001123768661350.227643702708-0.005705230266780.008222619788250.246044873247-0.008247023927980.20044519454430.996470844419.945618055920.5906900643
30.002029945990250.01021290314340.004999229715120.05181361566340.02924822123640.04085812582290.1773225939920.4367441273570.245736377344-0.394042376297-0.170943830288-0.07245892358-0.2632500349590.439555666947-0.001906017976620.305141454777-0.00208075134099-0.001852100903150.362964426430.08429628633470.28089680648650.037910624733.745655925912.5424922859
40.8090816010380.321884134131-0.1024950787490.407986891556-0.5807911023571.0541916178-0.0175186900417-0.03277066507410.005292903927520.0414103880948-0.0508491638019-0.0492085855685-0.05410301062560.154981191427-3.26225875497E-50.1548026627440.00972922528077-0.02111351050970.181895824333-0.002118493722750.18263569644948.141480773121.882426199727.4189983799
50.1166422397760.1427478954530.04939105754180.3027942828250.2086132491210.173279507753-0.1124408248090.124842377874-0.0565811655908-0.01635725895390.001745172572720.1201606428240.109314264415-0.1160687664070.0001169845101680.2070292828130.02201205265570.0001577136559220.2144487773590.002612500966340.1913220312832.57094717725.554521086824.8598843406
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 364 )0 - 3641 - 66
22chain 'A' and (resid 365 through 400 )365 - 40067 - 102
33chain 'A' and (resid 401 through 412 )401 - 412103 - 114
44chain 'A' and (resid 413 through 497 )413 - 497115 - 199
55chain 'A' and (resid 498 through 510 )498 - 510200 - 212

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