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- PDB-4zd5: Catalytic domain of Sst2 F403A mutant -

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Basic information

Entry
Database: PDB / ID: 4zd5
TitleCatalytic domain of Sst2 F403A mutant
ComponentsAMSH-like protease sst2
KeywordsHYDROLASE / helix-beta-helix sandwich Zinc metalloprotease endosome Ubiquitin
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: 2.07 Å
AuthorsShrestha, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1R01RR026273 United States
CitationJournal: To Be Published
Title: Structure of the catalytic domain of Sst2 F403A mutant at 2.07 Angstoms resolution
Authors: Shrestha, R.K.
History
DepositionApr 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_detector.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)44,38311
Polymers43,8112
Non-polymers5729
Water1,67593
1
A: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2857
Polymers21,9061
Non-polymers3796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0994
Polymers21,9061
Non-polymers1933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.646, 74.898, 64.587
Angle α, β, γ (deg.)90.00, 112.91, 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: 21905.637 Da / Num. of mol.: 2 / Fragment: unp residues 245-435 / Mutation: F403A
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 / Details (production host): 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M sodium citrate tribasic diehydrate, 20%w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2014
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: 2.07→59.5 Å / Num. obs: 31003 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.02 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MS7

4ms7


Resolution: 2.07→59.49 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.021 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24059 1530 5 %RANDOM
Rwork0.19988 ---
obs0.20192 28834 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.592 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.07→59.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 24 93 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193016
X-RAY DIFFRACTIONr_bond_other_d0.0020.023004
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.974097
X-RAY DIFFRACTIONr_angle_other_deg0.8773.0016929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7524.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16415530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9221511
X-RAY DIFFRACTIONr_chiral_restr0.1110.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02658
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7033.0751514
X-RAY DIFFRACTIONr_mcbond_other2.7033.0751513
X-RAY DIFFRACTIONr_mcangle_it3.8334.5961900
X-RAY DIFFRACTIONr_mcangle_other3.8324.5971901
X-RAY DIFFRACTIONr_scbond_it3.2933.3571502
X-RAY DIFFRACTIONr_scbond_other3.2933.3571502
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9414.8962197
X-RAY DIFFRACTIONr_long_range_B_refined6.61524.3713301
X-RAY DIFFRACTIONr_long_range_B_other6.61424.3753302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.069→2.123 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 88 -
Rwork0.289 1611 -
obs--74.22 %

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