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- PDB-7lm3: Crystal Structure of Thr316Ala mutant of JAMM domain of S. pombe -

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Basic information

Entry
Database: PDB / ID: 7lm3
TitleCrystal Structure of Thr316Ala mutant of JAMM domain of S. pombe
ComponentsAMSH-like protease sst2
KeywordsMETAL BINDING PROTEIN / Deubiquitinating enzymes / JAMM domain / ESCRT complexes / Lus63-linked polyubiquitin chains
Function / homology
Function and homology information


Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site ...Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / 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 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile.
Similarity search - Domain/homology
PHOSPHATE ION / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShrestha, R. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01RR026273 United States
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis.
Authors: Shrestha, R. / Das, C.
#1: Journal: 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.
#2: Journal: Biochemistry / Year: 2015
Title: Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase.
Authors: Bueno, A.N. / Shrestha, R.K. / Ronau, J.A. / Babar, A. / Sheedlo, M.J. / Fuchs, J.E. / Paul, L.N. / Das, C.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,3558
Polymers43,9032
Non-polymers4526
Water0
1
A: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1774
Polymers21,9521
Non-polymers2263
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1774
Polymers21,9521
Non-polymers2263
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.531, 121.338, 57.145
Angle α, β, γ (deg.)90.000, 129.581, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 21951.707 Da / Num. of mol.: 2 / Mutation: T316A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: sst2, SPAC19B12.10 / Production host: Escherichia coli (E. coli)
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium phosphate dibasic (pH 8.0), 20% w/v polyethylene glycol 3,350 with 40% v/v Polypropylene glycol P400 as an additive

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12793 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.043 / Rrim(I) all: 0.086 / Χ2: 1.109 / Net I/σ(I): 9 / Num. measured all: 49946
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.90.7216160.7860.4250.8381.00397.5
2.75-2.83.90.6466700.8320.3790.7490.981100
2.8-2.853.90.6066050.8880.3530.7010.93796.2
2.85-2.913.90.576500.8790.3330.6611.00599.4
2.91-2.973.90.4636220.9110.2690.5360.98899.5
2.97-3.043.90.3456270.960.2010.41.1296.9
3.04-3.123.90.2616490.9780.1520.3021.072100
3.12-3.23.90.216250.9840.1230.2441.17196.7
3.2-3.340.166440.9850.0930.1851.067100
3.3-3.43.90.1386300.9880.080.1591.19997.7
3.4-3.523.90.1096360.9910.0640.1261.262100
3.52-3.663.90.0876300.9950.050.11.15198
3.66-3.833.90.0686520.9970.040.0781.11698.5
3.83-4.033.90.0596360.9980.0340.0681.042100
4.03-4.293.90.056450.9980.0290.0580.96898.8
4.29-4.623.80.0376570.9980.0220.0430.91799.2
4.62-5.083.90.046380.9980.0240.0470.99499.2
5.08-5.813.90.0436610.9980.0250.051.29199.2
5.81-7.323.90.0426320.9980.0240.0481.43699.4
7.32-503.80.0286680.9990.0170.0331.45699.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX19.1refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JXE

4jxe


Resolution: 2.7→44.04 Å / SU ML: 0.5618 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 32.4016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2529 624 4.88 %
Rwork0.2006 12161 -
obs0.2033 12785 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.42 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 14 0 2826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972888
X-RAY DIFFRACTIONf_angle_d1.13923936
X-RAY DIFFRACTIONf_chiral_restr0.0579465
X-RAY DIFFRACTIONf_plane_restr0.0094499
X-RAY DIFFRACTIONf_dihedral_angle_d6.9164385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.42341520.3472999X-RAY DIFFRACTION98.04
2.97-3.40.30621480.28063025X-RAY DIFFRACTION98.27
3.4-4.280.28141570.1933050X-RAY DIFFRACTION99.07
4.28-44.040.19791670.15653087X-RAY DIFFRACTION99.12
Refinement TLS params.Method: refined / Origin x: -29.3808393257 Å / Origin y: 19.8688518798 Å / Origin z: 12.6805998767 Å
111213212223313233
T0.53286141467 Å20.00483986899071 Å2-0.0186628162998 Å2-0.614750384001 Å2-0.00240953282505 Å2--0.568489512228 Å2
L0.0873106998806 °20.240386729053 °2-0.103156123205 °2-2.06415581877 °2-0.156362297622 °2--0.111598393973 °2
S0.0196054589299 Å °0.00155602167757 Å °-0.0185859350088 Å °-0.117555004189 Å °-0.0463896830924 Å °0.217322997639 Å °-0.0297291110274 Å °-0.00228425548995 Å °0.0209739265025 Å °
Refinement TLS groupSelection details: all

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