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- PDB-3p7l: Rat Insulin Degrading Enzyme (Insulysin) -

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Basic information

Entry
Database: PDB / ID: 3p7l
TitleRat Insulin Degrading Enzyme (Insulysin)
ComponentsInsulin-degrading enzyme
KeywordsHYDROLASE / peptidase
Function / homology
Function and homology information


beta-endorphin binding / Peroxisomal protein import / Insulin receptor recycling / insulysin / Ub-specific processing proteases / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process ...beta-endorphin binding / Peroxisomal protein import / Insulin receptor recycling / insulysin / Ub-specific processing proteases / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / cytosolic proteasome complex / ubiquitin-modified protein reader activity / insulin binding / regulation of aerobic respiration / insulin receptor recycling / peptide catabolic process / amyloid-beta clearance / peptide hormone binding / peroxisomal matrix / amyloid-beta metabolic process / proteolysis involved in protein catabolic process / endosome lumen / negative regulation of proteolysis / peptide binding / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / peroxisome / peptidase activity / amyloid-beta binding / basolateral plasma membrane / endopeptidase activity / response to oxidative stress / external side of plasma membrane / protein-containing complex binding / cell surface / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular exosome / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Insulin-degrading enzyme
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0776 Å
AuthorsRodgers, D.W. / Noinaj, N.
CitationJournal: Plos One / Year: 2011
Title: Identification of the allosteric regulatory site of insulysin.
Authors: Noinaj, N. / Bhasin, S.K. / Song, E.S. / Scoggin, K.E. / Juliano, M.A. / Juliano, L. / Hersh, L.B. / Rodgers, D.W.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Insulin-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3752
Polymers113,3091
Non-polymers651
Water4,089227
1
A: Insulin-degrading enzyme
hetero molecules

A: Insulin-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,7504
Polymers226,6192
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.61, 70.98, 114.00
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Insulin-degrading enzyme / Insulin protease / Insulinase / Insulysin


Mass: 113309.453 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-1019
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ide / Production host: Escherichia coli (E. coli) / References: UniProt: P35559, insulysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium citrate pH 6.5, 100 mM ammonium acetate, and 20% PEG 4000, 8 mg/ml protein, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9718 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2008
RadiationMonochromator: Si(111) sagitally focused / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 2.077→50 Å / Num. all: 55754 / Num. obs: 54422 / % possible obs: 97.6 % / Observed criterion σ(F): -0.81 / Observed criterion σ(I): -0.25
Reflection shellResolution: 2.077→2.16 Å / % possible all: 87.9

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.0776→41.966 Å / SU ML: 0.32 / σ(F): 1.46 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 2650 5.06 %random
Rwork0.2023 ---
all0.2162 55754 --
obs0.2057 52364 93.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.207 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.724 Å2-0 Å24.1655 Å2
2--2.9813 Å20 Å2
3----1.2574 Å2
Refinement stepCycle: LAST / Resolution: 2.0776→41.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 1 227 8030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087999
X-RAY DIFFRACTIONf_angle_d1.11210820
X-RAY DIFFRACTIONf_dihedral_angle_d14.893029
X-RAY DIFFRACTIONf_chiral_restr0.0711159
X-RAY DIFFRACTIONf_plane_restr0.0051403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0776-2.15190.39462230.32884178X-RAY DIFFRACTION79
2.1519-2.2380.31622690.284744X-RAY DIFFRACTION91
2.238-2.33990.32612530.25264842X-RAY DIFFRACTION92
2.3399-2.46320.32322450.24214866X-RAY DIFFRACTION93
2.4632-2.61750.32072610.2395022X-RAY DIFFRACTION95
2.6175-2.81960.30052510.22835056X-RAY DIFFRACTION95
2.8196-3.10330.2792990.20915103X-RAY DIFFRACTION97
3.1033-3.55210.25792870.18025238X-RAY DIFFRACTION99
3.5521-4.47450.20892770.1555279X-RAY DIFFRACTION99
4.4745-41.97460.2292850.16555386X-RAY DIFFRACTION99

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