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- PDB-4ms7: Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4ms7
TitleCrystal structure of Schizosaccharomyces pombe sst2 catalytic domain
ComponentsAMSH-like protease sst2
KeywordsHYDROLASE / Helix-beta-helix sandwich / ubiquitin / dequbiquitination / Zinc metalloprotease / 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
AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.673 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 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)44,72013
Polymers43,9632
Non-polymers75611
Water4,846269
1
A: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4838
Polymers21,9821
Non-polymers5017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2375
Polymers21,9821
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.150, 69.391, 61.971
Angle α, β, γ (deg.)90.00, 104.73, 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: 21981.732 Da / Num. of mol.: 2 / 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
#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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium phosphate dibasic, 20 % w/v polyethylene glycol 3350, 30% w/v 1,6- hexanedio, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 8.0

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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: 1.67→50 Å / Num. all: 53232 / Num. obs: 51582 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 20.8
Reflection shellResolution: 1.67→1.7 Å / % possible all: 90.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.673→29.967 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 2627 5.09 %Random
Rwork0.1772 ---
all0.1772 53166 --
obs0.1788 51576 97.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.673→29.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 36 269 3249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063084
X-RAY DIFFRACTIONf_angle_d1.1214176
X-RAY DIFFRACTIONf_dihedral_angle_d12.8041143
X-RAY DIFFRACTIONf_chiral_restr0.072487
X-RAY DIFFRACTIONf_plane_restr0.006523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.673-1.70320.25651410.21722386X-RAY DIFFRACTION92
1.7032-1.7360.23391530.19832480X-RAY DIFFRACTION95
1.736-1.77140.22591200.19922549X-RAY DIFFRACTION96
1.7714-1.80990.22511430.1962525X-RAY DIFFRACTION96
1.8099-1.8520.19581500.17892541X-RAY DIFFRACTION96
1.852-1.89830.22281200.17992541X-RAY DIFFRACTION96
1.8983-1.94970.2161500.18562545X-RAY DIFFRACTION96
1.9497-2.0070.23221300.18682577X-RAY DIFFRACTION97
2.007-2.07180.24191450.18612548X-RAY DIFFRACTION97
2.0718-2.14580.21521380.18842559X-RAY DIFFRACTION97
2.1458-2.23170.20471170.17632625X-RAY DIFFRACTION97
2.2317-2.33320.20991280.18432611X-RAY DIFFRACTION98
2.3332-2.45620.19071300.18662582X-RAY DIFFRACTION98
2.4562-2.610.21451590.18652596X-RAY DIFFRACTION98
2.61-2.81140.21591430.18032627X-RAY DIFFRACTION98
2.8114-3.0940.2231410.18962637X-RAY DIFFRACTION99
3.094-3.54110.19251290.18082648X-RAY DIFFRACTION99
3.5411-4.45910.19221500.15522673X-RAY DIFFRACTION99
4.4591-29.97180.21861400.16152699X-RAY DIFFRACTION99

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