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- PDB-2d5u: Solution structure of the N-terminal portion of the PUB domain of... -

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Basic information

Entry
Database: PDB / ID: 2d5u
TitleSolution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase
ComponentsN-glycanase 1
KeywordsHYDROLASE / PNGase
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / glycoprotein catabolic process / collagen-containing extracellular matrix / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide N glycanase, PAW domain / PAW domain superfamily / PNGase C-terminal domain, mannose-binding module PAW / PAW domain profile. / domain present in PNGases and other hypothetical proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / PUB domain / PUB-like domain superfamily / PUB domain ...Peptide N glycanase, PAW domain / PAW domain superfamily / PNGase C-terminal domain, mannose-binding module PAW / PAW domain profile. / domain present in PNGases and other hypothetical proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / PUB domain / PUB-like domain superfamily / PUB domain / domain in protein kinases, N-glycanases and other nuclear proteins / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Papain-like cysteine peptidase superfamily / Galactose-binding-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsSasakawa, H. / Hirao, T. / Yamaguchi, Y. / Suzuki, T. / Kato, K.
CitationJournal: To be Published
Title: Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase
Authors: Sasakawa, H. / Hirao, T. / Yamaguchi, Y. / Suzuki, T. / Kato, K.
History
DepositionNov 6, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-glycanase 1


Theoretical massNumber of molelcules
Total (without water)13,4651
Polymers13,4651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein N-glycanase 1


Mass: 13465.267 Da / Num. of mol.: 1 / Fragment: PUB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codonplus
References: GenBank: 31981178, UniProt: Q9JI78*PLUS, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated ROESY
1213D 15N-separated NOESY
1322D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM N-terminal portion of the PUB domain U-15N,13C; 10mM MES, 90% H2O, 10% D2O90% H2O/10% D2O
21.0mM N-terminal portion of the PUB domain; 10mM MES, 99% D2O99% D2O
Sample conditionsIonic strength: 5 / pH: 5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.8collection
NMRPipe2004513Delaglioprocessing
Olivia1.1Yokochidata analysis
CYANA2Guntertstructure solution
CYANA2Guntertrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1460 restraints, 1272 are NOE-derived distance constraints, 152 dihedral angle restraints, 36 distance restraints for hydrogen bonds.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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