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- PDB-4msj: Crystal structure of S. pombe AMSH-like protease SST2 catalytic d... -

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Basic information

Entry
Database: PDB / ID: 4msj
TitleCrystal structure of S. pombe AMSH-like protease SST2 catalytic domain from P212121 space group
ComponentsAMSH-like protease sst2
KeywordsHYDROLASE / helix-beta-helix sandwich / ubiquitin / deubiquitination / zinc metalloprotease / 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 / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / 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 / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / 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
GLYCINE / PHOSPHATE ION / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,19421
Polymers65,9453
Non-polymers1,24918
Water3,927218
1
A: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,68811
Polymers21,9821
Non-polymers70610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2375
Polymers21,9821
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2705
Polymers21,9821
Non-polymers2884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.799, 58.066, 187.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 21981.732 Da / Num. of mol.: 3 / Fragment: catalytic domain, UNP residues 245-435
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

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Non-polymers , 5 types, 236 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium phosphate dibasic, 20% w/v PEG 3350, 1.0 M glycine, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 2012
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: 1.8→50 Å / Num. all: 56615 / Num. obs: 55256 / % possible obs: 97.9 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 6 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 17.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.628 / % possible all: 96.6

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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 CODE 4JXE

4jxe


Resolution: 1.8→47.31 Å / SU ML: 0.19 / σ(F): 1.37 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 2809 5.09 %
Rwork0.2015 --
obs0.2033 55187 97.44 %
all-56637 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4428 0 58 218 4704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084582
X-RAY DIFFRACTIONf_angle_d1.1466202
X-RAY DIFFRACTIONf_dihedral_angle_d13.7471682
X-RAY DIFFRACTIONf_chiral_restr0.079723
X-RAY DIFFRACTIONf_plane_restr0.005776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82940.28761130.24822335X-RAY DIFFRACTION87
1.8294-1.86270.321480.23872520X-RAY DIFFRACTION97
1.8627-1.89850.26481480.23952575X-RAY DIFFRACTION97
1.8985-1.93730.23891300.22932559X-RAY DIFFRACTION96
1.9373-1.97940.31371350.2292562X-RAY DIFFRACTION98
1.9794-2.02550.23841240.22522598X-RAY DIFFRACTION97
2.0255-2.07610.2841400.22622541X-RAY DIFFRACTION96
2.0761-2.13230.28271490.22662586X-RAY DIFFRACTION98
2.1323-2.1950.26981330.22332589X-RAY DIFFRACTION97
2.195-2.26580.24211480.21582600X-RAY DIFFRACTION97
2.2658-2.34680.2591270.22082631X-RAY DIFFRACTION98
2.3468-2.44080.28241310.21512609X-RAY DIFFRACTION98
2.4408-2.55190.25181350.22582651X-RAY DIFFRACTION99
2.5519-2.68640.26421400.22522660X-RAY DIFFRACTION99
2.6864-2.85470.22271480.2252688X-RAY DIFFRACTION99
2.8547-3.07510.27371510.22652674X-RAY DIFFRACTION99
3.0751-3.38440.27081530.21032680X-RAY DIFFRACTION99
3.3844-3.8740.20711440.19082728X-RAY DIFFRACTION99
3.874-4.880.18431490.15252719X-RAY DIFFRACTION99
4.88-47.32610.21151630.17382873X-RAY DIFFRACTION99

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