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

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Basic information

Entry
Database: PDB / ID: 4jxe
TitleCrystal structure of Schizosaccharomyces pombe sst2 catalytic domain
ComponentsAMSH-like protease sst2
KeywordsHYDROLASE / Helix-beta-helix sandwich / ubiquitin / dequbiquitination / Zinc metalloprotease / deubiquitination / 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 deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding ...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 deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / 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 / MOLECULAR REPLACEMENT / Resolution: 1.451 Å
AuthorsShrestha, R.K. / 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
DepositionMar 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Sep 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,84214
Polymers43,9632
Non-polymers87812
Water3,837213
1
A: 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
2
B: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6059
Polymers21,9821
Non-polymers6238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.139, 69.436, 62.018
Angle α, β, γ (deg.)90.00, 104.84, 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 (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.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium phosphate dibasic, 20 % w/v polyethylene glycol 3,350 , 30% w/v 1,6- hexanediol , VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8

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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: 1.45→29.64 Å / Num. all: 81050 / Num. obs: 80642 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 19.28
Reflection shellResolution: 1.45→1.48 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREP(ccp4)phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZNR

2znr


Resolution: 1.451→29.64 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 4035 5 %random
Rwork0.1627 ---
obs0.1642 80642 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.451→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 44 213 3209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053134
X-RAY DIFFRACTIONf_angle_d1.0524259
X-RAY DIFFRACTIONf_dihedral_angle_d13.4671185
X-RAY DIFFRACTIONf_chiral_restr0.067499
X-RAY DIFFRACTIONf_plane_restr0.005531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4512-1.46830.24451140.18972518X-RAY DIFFRACTION95
1.4683-1.48620.25841310.20072596X-RAY DIFFRACTION98
1.4862-1.5050.23991460.18472603X-RAY DIFFRACTION98
1.505-1.52480.22841340.18032600X-RAY DIFFRACTION99
1.5248-1.54570.27071330.17042632X-RAY DIFFRACTION98
1.5457-1.56780.22661080.16462677X-RAY DIFFRACTION99
1.5678-1.59120.19991210.15042625X-RAY DIFFRACTION99
1.5912-1.6160.18531240.14792644X-RAY DIFFRACTION99
1.616-1.64250.20741490.14252627X-RAY DIFFRACTION99
1.6425-1.67090.19731510.1432598X-RAY DIFFRACTION99
1.6709-1.70120.2171420.14272612X-RAY DIFFRACTION99
1.7012-1.7340.18641470.13912615X-RAY DIFFRACTION99
1.734-1.76930.14861500.13682659X-RAY DIFFRACTION99
1.7693-1.80780.20431440.13532629X-RAY DIFFRACTION99
1.8078-1.84990.17021300.13862661X-RAY DIFFRACTION100
1.8499-1.89610.18271400.14622640X-RAY DIFFRACTION100
1.8961-1.94740.19941510.14862650X-RAY DIFFRACTION100
1.9474-2.00470.19621460.15192654X-RAY DIFFRACTION100
2.0047-2.06940.17251550.15472623X-RAY DIFFRACTION100
2.0694-2.14330.19411470.16172650X-RAY DIFFRACTION100
2.1433-2.22910.18941490.15532649X-RAY DIFFRACTION100
2.2291-2.33050.18741390.16042679X-RAY DIFFRACTION100
2.3305-2.45330.19791310.17272671X-RAY DIFFRACTION100
2.4533-2.60690.18861340.17192670X-RAY DIFFRACTION100
2.6069-2.80810.19591280.17682688X-RAY DIFFRACTION100
2.8081-3.09040.2191470.18892671X-RAY DIFFRACTION100
3.0904-3.53690.19861410.17892679X-RAY DIFFRACTION100
3.5369-4.45380.18121570.15512688X-RAY DIFFRACTION100
4.4538-29.65470.1721460.15972699X-RAY DIFFRACTION99

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