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- PDB-2hpj: Crystal structure of the PUB domain of mouse PNGase -

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Basic information

Entry
Database: PDB / ID: 2hpj
TitleCrystal structure of the PUB domain of mouse PNGase
ComponentsPNGase
KeywordsHYDROLASE / PUB domain / Winged helix
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsZhao, G. / Zhou, X. / Wang, L. / Li, G. / Lennarz, W. / Schindelin, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Studies on peptide:N-glycanase-p97 interaction suggest that p97 phosphorylation modulates endoplasmic reticulum-associated degradation.
Authors: Zhao, G. / Zhou, X. / Wang, L. / Li, G. / Schindelin, H. / Lennarz, W.J.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: PNGase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4805
Polymers11,1121
Non-polymers3684
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.641, 52.042, 34.946
Angle α, β, γ (deg.)90.000, 115.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PNGase / Peptide N-glycanase


Mass: 11111.675 Da / Num. of mol.: 1 / Fragment: Residues 12-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngly1 / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Codon Plus RIL
References: UniProt: Q9JI78, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18-22% PEG 5000 MME and 14-18% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONNSLS X26C21.0074
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEMar 10, 2006
ADSC QUANTUM 42CCDMar 29, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.00741
ReflectionRedundancy: 7.7 % / Av σ(I) over netI: 36.5 / Number: 38504 / Rmerge(I) obs: 0.052 / Χ2: 1.07 / D res high: 2.28 Å / D res low: 50 Å / Num. obs: 4969 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.915098.510.0571.2467.3
3.94.9199.410.0471.1417.6
3.413.999.410.0460.8787.8
3.093.4199.810.050.9587.9
2.873.0999.610.0520.9917.9
2.72.8799.810.0551.0247.9
2.572.799.410.0591.1117.9
2.462.5799.410.0621.1327.9
2.362.4699.410.0681.0997.9
2.282.3698.610.0731.1677.3
ReflectionResolution: 1.7→50 Å / Num. obs: 11390 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.08 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Χ2: 1.714 / Net I/σ(I): 23.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 6.6 / Num. unique all: 682 / Rsym value: 0.106 / Χ2: 1.065 / % possible all: 56.8

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Phasing

PhasingMethod: SIRAS
Phasing setD res high: 2.5 Å / D res low: 30 Å
Phasing dmFOM : 0.77 / FOM acentric: 0.77 / FOM centric: 0.77 / Reflection: 3767 / Reflection acentric: 3515 / Reflection centric: 252
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-21.8560.930.920.9816613927
4.5-7.10.860.870.7551446450
3.6-4.50.880.880.8964259646
3.1-3.60.830.830.8464260240
2.7-3.10.710.710.71125106758
2.5-2.70.620.620.5267864731
Phasing MIRResolution: 2.5→30 Å / FOM: 0.49 / Reflection: 3767
Phasing MIR der
IDResolution (Å)Der set-IDNative set-ID
12.5-3011
21
Phasing MIR der site

ID: 1 / Atom type symbol: Hg

Der-IDBiso (Å)Fract xFract yFract zOccupancy
125.75140.416700.08330.2507
220.31950.86170.45090.01830.2004
Phasing MIR shell
Resolution (Å)FOMReflection
8.86-300.69185
5.64-8.860.62313
4.42-5.640.57406
3.76-4.420.49461
3.32-3.760.51530
3.01-3.320.47590
2.77-3.010.45629
2.58-2.770.38653

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.602 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 544 4.8 %RANDOM
Rwork0.147 ---
all0.149 10843 --
obs0.148 11387 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20.03 Å2
2--0.11 Å20 Å2
3----1.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.091 Å0.094 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms779 0 24 129 932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022811
X-RAY DIFFRACTIONr_bond_other_d0.0020.02768
X-RAY DIFFRACTIONr_angle_refined_deg1.5292.0081088
X-RAY DIFFRACTIONr_angle_other_deg0.91331788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70623.88936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85615145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.56157
X-RAY DIFFRACTIONr_chiral_restr0.10.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02156
X-RAY DIFFRACTIONr_nbd_refined0.2260.2191
X-RAY DIFFRACTIONr_nbd_other0.1870.2808
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2390
X-RAY DIFFRACTIONr_nbtor_other0.0830.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.223
X-RAY DIFFRACTIONr_mcbond_it1.2771.5643
X-RAY DIFFRACTIONr_mcbond_other0.2821.5199
X-RAY DIFFRACTIONr_mcangle_it1.3782800
X-RAY DIFFRACTIONr_scbond_it2.5233354
X-RAY DIFFRACTIONr_scangle_it3.5224.5288
LS refinement shellResolution: 1.7→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 21 -
Rwork0.197 413 -
obs-434 49.49 %
Refinement TLS params.Method: refined / Origin x: 40.9494 Å / Origin y: 51.83 Å / Origin z: 13.8017 Å
111213212223313233
T0.0074 Å20.007 Å20.0011 Å2-0.0133 Å2-0.0019 Å2--0.0091 Å2
L0.5072 °20.0713 °2-0.2753 °2-1.3981 °20.1354 °2--1.0417 °2
S-0.0073 Å °0.0059 Å °0.0303 Å °0.0128 Å °-0.0165 Å °-0.0211 Å °-0.015 Å °-0.0213 Å °0.0238 Å °
Refinement TLS groupSelection: ALL

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