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- PDB-7oiy: Crystal structure of the ZUFSP family member Mug105 -

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Basic information

Entry
Database: PDB / ID: 7oiy
TitleCrystal structure of the ZUFSP family member Mug105
ComponentsUbiquitin carboxyl-terminal hydrolase mug105
KeywordsHYDROLASE / ZUFSP / deubiquitinase / Schizosaccharomyces pombe / fission yeast / cysteine peptidase / K48
Function / homology
Function and homology information


ubiquitin-like protein peptidase activity / K48-linked deubiquitinase activity / meiotic cell cycle / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cytoplasm
Similarity search - Function
: / Cathepsin B; Chain A - #130 / Peptidase C78, ubiquitin fold modifier-specific peptidase 1/ 2 / Peptidase family C78 / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase mug105
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPichlo, C. / Hermanns, T. / Hofmann, K. / Baumann, U.
CitationJournal: 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
DepositionMay 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase mug105
B: Ubiquitin carboxyl-terminal hydrolase mug105
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2744
Polymers56,2282
Non-polymers462
Water5,423301
1
A: Ubiquitin carboxyl-terminal hydrolase mug105
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1372
Polymers28,1141
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase mug105
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1372
Polymers28,1141
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.235, 88.235, 111.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 3 or resid 5...
d_2ens_1(chain "B" and (resid 1 through 3 or resid 5...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETLYSLYSAA1 - 31 - 3
d_12LEULEUARGARGAA5 - 105 - 10
d_13LEULEUTHRTHRAA12 - 5712 - 57
d_14PROPROILEILEAA59 - 7359 - 73
d_15SERSERLYSLYSAA75 - 10375 - 103
d_16ILEILELEULEUAA105 - 160105 - 160
d_17PHEPHEGLYGLYAA162 - 164162 - 164
d_18SERSERLYSLYSAA166 - 208166 - 208
d_19SERSERPHEPHEAA210 - 213210 - 213
d_110GLNGLNPHEPHEAA215 - 244215 - 244
d_21METMETLYSLYSBB1 - 31 - 3
d_22LEULEUARGARGBB5 - 105 - 10
d_23LEULEUTHRTHRBB12 - 5712 - 57
d_24PROPROILEILEBB59 - 7359 - 73
d_25SERSERLYSLYSBB75 - 10375 - 103
d_26ILEILELEULEUBB105 - 160105 - 160
d_27PHEPHEGLYGLYBB162 - 164162 - 164
d_28SERSERLYSLYSBB166 - 208166 - 208
d_29SERSERPHEPHEBB210 - 213210 - 213
d_210GLNGLNPHEPHEBB215 - 244215 - 244

NCS oper: (Code: givenMatrix: (0.870582423948, 0.492021083531, 0.00122330432373), (0.491636736598, -0.869995430659, 0.0374335392294), (0.019482359704, -0.0319875599737, -0.999298370692)Vector: -104. ...NCS oper: (Code: given
Matrix: (0.870582423948, 0.492021083531, 0.00122330432373), (0.491636736598, -0.869995430659, 0.0374335392294), (0.019482359704, -0.0319875599737, -0.999298370692)
Vector: -104.026418491, 269.428672502, 30.445560095)

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase mug105 / Lys-48-selective deubiquitinase mug105 / DUB / Meiotically up-regulated gene 105 protein


Mass: 28113.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mug105, SPAC25H1.04 / Production host: Escherichia coli (E. coli) / References: UniProt: O13979, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.8 M sodium acetate pH 7.0; 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→39.46 Å / Num. obs: 53097 / % possible obs: 99.76 % / Redundancy: 6 % / Biso Wilson estimate: 34.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.35
Reflection shellResolution: 2.05→2.124 Å / Num. unique obs: 5246 / CC1/2: 0.441

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDS20180126data reduction
XDS20180126data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EI1

6ei1


Resolution: 2.05→39.46 Å / SU ML: 0.2341 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 22.3601
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2039 2000 3.77 %
Rwork0.1726 51081 -
obs0.1738 53081 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.57 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 2 301 4259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264149
X-RAY DIFFRACTIONf_angle_d0.50055619
X-RAY DIFFRACTIONf_chiral_restr0.0422587
X-RAY DIFFRACTIONf_plane_restr0.0029727
X-RAY DIFFRACTIONf_dihedral_angle_d12.44421474
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.72699417888 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.35781380.30063599X-RAY DIFFRACTION99.15
2.1-2.160.26961420.27713651X-RAY DIFFRACTION100
2.16-2.220.27111460.25093627X-RAY DIFFRACTION100
2.22-2.290.291460.23113660X-RAY DIFFRACTION100
2.29-2.380.24531390.22333628X-RAY DIFFRACTION99.95
2.38-2.470.25361410.21693642X-RAY DIFFRACTION99.97
2.47-2.580.27841470.20363667X-RAY DIFFRACTION99.95
2.58-2.720.23281430.20173615X-RAY DIFFRACTION99.95
2.72-2.890.23751430.18913659X-RAY DIFFRACTION100
2.89-3.110.19971460.18413659X-RAY DIFFRACTION99.97
3.11-3.430.22061430.16643638X-RAY DIFFRACTION99.24
3.43-3.920.16531470.12983639X-RAY DIFFRACTION99.08
3.92-4.940.1511420.12063681X-RAY DIFFRACTION99.97
4.94-39.460.15331370.1543716X-RAY DIFFRACTION99.59
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)
13.508883444684.54172217612-3.621367981526.88144868386-6.493118535466.989038051440.3010953188310.6596784852310.872047588902-0.05893382900180.2730989097380.847513334111-0.622582181904-0.907617526012-0.4728389915810.3539605509550.1835051093290.1141542473920.5096162305890.05916476877110.5021465232729.3529180981161.3045290564.39421934714
22.366794420070.249335038434-0.9284108367061.6098839166-1.713714046364.436008307470.0933550716479-0.0477362270990.2525094906910.09418424461840.0245880487650.0510109590776-0.338134963-0.101846474944-0.07823393218630.2292793992930.03073679025370.04373741536030.19955493483-0.003148632268120.27674305479531.3240101222151.02760919315.6181371043
32.048947114681.91160942999-1.51307022228.52050125231-0.1921188571875.131138355490.0244348192805-0.236454684788-0.05455084807480.325227894464-0.0782677825276-0.694837170804-0.005743706260910.5040574067140.04379883895850.258441656357-0.0256518684485-0.01949865749290.3525602562840.02803460970140.27584511308140.1775851354141.5724083928.9191326041
42.789605754150.164190936198-2.296724537641.57035159005-0.4839597175653.82271615082-0.0556583127903-0.0893799971785-0.0878136999148-0.00206097733196-0.0605957679821-0.1767542051340.01262048339160.205878373570.1112060857770.2244415017040.0104820368050.01269772465120.244884873192-0.01324211919190.21352085411647.2011896115145.34287663410.3659717095
56.773354418260.784479488842-0.3922243975567.23686762759-0.1451909565687.821945314090.1272256000250.2590230464-0.1817523911310.100277208574-0.07162032007610.1843651035740.457800400556-0.142810281268-0.01420593973530.1780049025230.02136551723470.0687791842480.234067246253-0.007862545130820.24252820942640.7057496571150.4672365817.1436323118
61.33457115954-0.9778632282621.419398899983.139619753-2.183112738522.048792128530.416125227678-0.09633123003190.919415892390.3720880942610.3180814909090.407937810123-1.10811093099-0.339481182719-0.6554316755780.5188646331220.01153122971120.2080807217080.3733112043520.009749575982170.56418897036338.8796086025164.04201962510.2057158137
74.06862114314-1.294588066060.3799184650165.39794489528-1.682205318773.667917201160.209951939017-0.3945712582240.8253003376390.2171538617620.0523442928194-0.174377859217-0.498439137187-0.0675442348897-0.1950234438360.332236123343-0.04181490140160.06876435123420.212201443344-0.03625491406240.39080837355347.1060864944163.30568578.72750079634
83.605245253960.665365716986-1.102048914021.546875526380.03681646420612.68415559528-0.2886590019060.00521611608162-0.5730032147390.2578223299670.0765575166658-0.0365919153930.6168727034140.1274433139180.1705220047050.3782388453220.03460293285010.06905783954630.22201690054-0.01625195082410.27298783552145.4116521284138.12322366411.9023280503
91.44702807396-1.506988483621.446582010772.08788035005-2.802612044624.700288947150.07943195273-0.0149372921016-0.120494518544-0.1433390617130.04737982645830.1075949655380.239049046721-0.111441390003-0.144471037870.291728131451-0.0417297395268-0.08337035944330.281109104363-0.02530116340570.336677898946-1.18825494162156.4125927778.44914663269
103.5265326986-0.7449561487391.641296364212.57974392516-0.06551457106983.584945474920.0349930548102-0.07456113667970.03247183663290.02919141886750.0499027899647-0.02596061077260.0338271073514-0.0490997336806-0.09843641793620.2031005169880.0118349537934-0.02607383420490.180943095928-0.01992212059480.1751588166187.66929076018163.45699782417.1390255957
111.88105320902-0.0537247842901-1.85900645175.83523828662-2.384840490392.856027682120.4830608973070.210587930571-0.408404945853-0.615953905735-0.05299126212460.09765680466820.8238314471670.0320411871008-0.4136010940410.480621957140.0611552909985-0.1896880619050.345542743263-0.04231490149660.43781702879.99607704127145.49656409815.5678733133
121.68710441904-0.07574050201550.003204353701732.084709421930.3420971812792.00542506310.0725766064125-0.0668965777090.0942796451095-0.252849982191-0.05360408191650.0735920591025-0.107232629511-0.0921189310151-0.02665156536960.2549413003130.0107637382803-0.0475411960120.218057036124-0.01914727146460.1806788092988.33366487412163.79202478615.9330300574
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 14 )AA1 - 141 - 14
22chain 'A' and (resid 15 through 72 )AA15 - 7215 - 72
33chain 'A' and (resid 73 through 106 )AA73 - 10673 - 106
44chain 'A' and (resid 107 through 146 )AA107 - 146107 - 146
55chain 'A' and (resid 147 through 173 )AA147 - 173147 - 173
66chain 'A' and (resid 174 through 196 )AA174 - 196174 - 196
77chain 'A' and (resid 197 through 214 )AA197 - 214197 - 214
88chain 'A' and (resid 215 through 244 )AA215 - 244215 - 244
99chain 'B' and (resid 1 through 106 )BB1 - 1061 - 106
1010chain 'B' and (resid 107 through 173 )BB107 - 173107 - 173
1111chain 'B' and (resid 174 through 196 )BB174 - 196174 - 196
1212chain 'B' and (resid 197 through 244 )BB197 - 244197 - 244

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