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- PDB-2ccq: The PUB domain functions as a p97 binding module in human peptide... -

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Basic information

Entry
Database: PDB / ID: 2ccq
TitleThe PUB domain functions as a p97 binding module in human peptide N-glycanase.
ComponentsPEPTIDE N-GLYCANASE HOMOLOG
KeywordsGLYCOPROTEIN / GLYCANASE HOMOLOG
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / : / glycoprotein catabolic process / protein deglycosylation / protein quality control for misfolded or incompletely synthesized proteins / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / protein folding / metal ion binding / nucleus ...peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / : / glycoprotein catabolic process / protein deglycosylation / protein quality control for misfolded or incompletely synthesized proteins / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / protein folding / metal ion binding / nucleus / 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-like domain superfamily / PUB domain / PUB domain / domain in protein kinases, N-glycanases and other nuclear proteins ...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-like domain superfamily / PUB domain / 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 / Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAllen, M.D. / Buchberger, A. / Bycroft, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Pub Domain Functions as a P97 Binding Module in Human Peptide N-Glycanase.
Authors: Allen, M.D. / Buchberger, A. / Bycroft, M.
History
DepositionJan 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE N-GLYCANASE HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3854
Polymers11,1091
Non-polymers2763
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.516, 73.516, 33.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PEPTIDE N-GLYCANASE HOMOLOG / P97


Mass: 11108.675 Da / Num. of mol.: 1 / Fragment: N-TERMINAL, RESIDUES 8-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9BVR8, UniProt: Q96IV0*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.31 Å3/Da / Density % sol: 47 %
Description: NATIVE STRUCTURE WAS SOLVED USING A SEMET STRUCTURE OF THE DOMAIN - DATA UNPUBLISHED
Crystal growpH: 8.5
Details: 0.2 M SODIUM ACETATE, 0.1 M TRIS (PH 8.5), 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→33 Å / Num. obs: 13734 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.4
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.7 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 679 5 %RANDOM
Rwork0.1932 ---
obs0.1932 13624 99.8 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 63.2506 Å2 / ksol: 0.400978 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.525 Å2-2.835 Å20 Å2
2---3.525 Å20 Å2
3---7.049 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 18 134 932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.559
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4BME.PAR
X-RAY DIFFRACTION5GOL.PAR

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