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- PDB-4msd: Crystal structure of Schizosaccharomyces pombe AMSH-like protein ... -

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Basic information

Entry
Database: PDB / ID: 4msd
TitleCrystal structure of Schizosaccharomyces pombe AMSH-like protein SST2 T319I mutant
ComponentsAMSH-like protease sst2
KeywordsHYDROLASE / Helix-beta-helix sandwich / ubiquitin / deubiquitination / zinc metalloprotease / AMSH / lysine 63-linked polyubiquitin / cytosol
Function / homology
Function and homology information


Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity ...Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site / ubiquitin binding / endosome / zinc ion binding / membrane / cytoplasm
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShrestha, R.K. / Ronau, J.A. / Das, C.
CitationJournal: Biochemistry / Year: 2014
Title: Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product.
Authors: Shrestha, R.K. / Ronau, J.A. / Davies, C.W. / Guenette, R.G. / Strieter, E.R. / Paul, L.N. / Das, C.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMSH-like protease sst2
B: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,27221
Polymers43,9882
Non-polymers1,28519
Water2,972165
1
A: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,71311
Polymers21,9941
Non-polymers72010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,55910
Polymers21,9941
Non-polymers5659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.048, 74.117, 64.865
Angle α, β, γ (deg.)90.00, 113.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AMSH-like protease sst2 / Suppressor of ste12 deletion protein 2


Mass: 21993.787 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 245-435 / Mutation: T319I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972/ATCC 24843 / Gene: sst2, SPAC19B12.10 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.03 M citric acid, 0.07 M bis-tris propane, pH 7.6, 20% PEG 3350, benzamidine hydrochloride (additive), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 39816 / Num. obs: 39816 / % possible obs: 100 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 18.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1996 / Rsym value: 0.565 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4JXE

4jxe


Resolution: 1.9→33.612 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 1995 5.01 %Random
Rwork0.1876 ---
all0.1891 39867 --
obs0.1876 39791 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 68 165 3139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073029
X-RAY DIFFRACTIONf_angle_d1.1224079
X-RAY DIFFRACTIONf_dihedral_angle_d14.5721124
X-RAY DIFFRACTIONf_chiral_restr0.071477
X-RAY DIFFRACTIONf_plane_restr0.005507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94720.31321380.26142626X-RAY DIFFRACTION98
1.9472-1.99980.28041470.24222692X-RAY DIFFRACTION100
1.9998-2.05870.28421410.22582691X-RAY DIFFRACTION100
2.0587-2.12510.26161350.21212679X-RAY DIFFRACTION100
2.1251-2.20110.21711330.20592699X-RAY DIFFRACTION100
2.2011-2.28920.20251390.19372702X-RAY DIFFRACTION100
2.2892-2.39330.23251240.19852724X-RAY DIFFRACTION100
2.3933-2.51950.23171290.2032714X-RAY DIFFRACTION100
2.5195-2.67730.23741230.20912695X-RAY DIFFRACTION100
2.6773-2.88390.25731640.20792686X-RAY DIFFRACTION100
2.8839-3.17390.24881670.20282686X-RAY DIFFRACTION100
3.1739-3.63270.19271520.19042730X-RAY DIFFRACTION100
3.6327-4.5750.15451460.15172711X-RAY DIFFRACTION100
4.575-33.61750.20711570.15662761X-RAY DIFFRACTION100

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