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- PDB-4zfr: Catalytic domain of Sst2 F403A mutant bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 4zfr
TitleCatalytic domain of Sst2 F403A mutant bound to ubiquitin
Components
  • AMSH-like protease sst2
  • ubiquitin
KeywordsHYDROLASE / Helix- beta- helix sandwich / ubiquitin / Zinc metalloprotease / cytosol / endosome
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 / symbiont entry into host cell via disruption of host cell glycocalyx / 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 / symbiont entry into host cell via disruption of host cell glycocalyx / K63-linked deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / symbiont entry into host cell via disruption of host cell envelope / cell division site / virus tail / 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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Pectin lyase fold / Pectin lyase fold/virulence factor ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Pectin lyase fold / Pectin lyase fold/virulence factor / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Ubiquitin family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail fiber / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 Catalytic domain of Sst2 F403A mutant bound to ubiquitin at 1.7 Angstroms
Authors: Shrestha, R.K.
History
DepositionApr 21, 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.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_conn.ptnr2_label_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: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1496
Polymers30,8942
Non-polymers2554
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-49 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.139, 58.174, 56.442
Angle α, β, γ (deg.)90.00, 109.30, 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.: 1 / 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-6-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein ubiquitin


Mass: 8988.284 Da / Num. of mol.: 1 / Fragment: unp residues 77-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pGEX-6-P1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium citrate tribasic diehydrate, 0.1M HEPES sodium, 20% v/v 2-propanol

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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: 1.719→53.27 Å / Num. obs: 26060 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 23.6
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.32 / % 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: 4K1R

4k1r


Resolution: 1.72→53.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.593 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1382 5 %RANDOM
Rwork0.201 ---
obs0.203 26060 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.72→53.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 10 43 2072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192073
X-RAY DIFFRACTIONr_bond_other_d0.0020.022045
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.9722812
X-RAY DIFFRACTIONr_angle_other_deg0.88134715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53424.76284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36315364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.62159
X-RAY DIFFRACTIONr_chiral_restr0.1140.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02444
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_it2.2092.3461047
X-RAY DIFFRACTIONr_mcbond_other2.2082.3451046
X-RAY DIFFRACTIONr_mcangle_it2.8973.5091307
X-RAY DIFFRACTIONr_mcangle_other2.8963.511308
X-RAY DIFFRACTIONr_scbond_it2.8382.6171026
X-RAY DIFFRACTIONr_scbond_other2.8372.6171026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0753.8021506
X-RAY DIFFRACTIONr_long_range_B_refined5.84918.3442167
X-RAY DIFFRACTIONr_long_range_B_other5.84918.3532168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 87 -
Rwork0.29 1939 -
obs--99.22 %
Refinement TLS params.Method: refined / Origin x: 17.428 Å / Origin y: 1.54 Å / Origin z: 17.376 Å
111213212223313233
T0.2211 Å2-0.0224 Å20.1177 Å2-0.0268 Å20.0053 Å2--0.0976 Å2
L1.3242 °20.2492 °20.1086 °2-3.8626 °20.1226 °2--2.0001 °2
S-0.1152 Å °0.094 Å °-0.031 Å °0.2188 Å °-0.0324 Å °-0.1791 Å °0.1066 Å °0.1446 Å °0.1476 Å °

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