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- PDB-2g9f: Crystal structure of intein-tagged mouse PNGase C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2g9f
TitleCrystal structure of intein-tagged mouse PNGase C-terminal domain
Componentspeptide N-glycanase
KeywordsHYDROLASE / beta-sandwich
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 / protein quality control for misfolded or incompletely synthesized proteins / collagen-containing extracellular matrix / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
PAW 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 / PUB-like domain superfamily / PUB domain / PUB domain / domain in protein kinases, N-glycanases and other nuclear proteins ...PAW 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 / 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 / Papain-like cysteine peptidase superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
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: 1.9 Å
AuthorsZhou, X. / Zhao, G. / Wang, L. / Li, G. / Lennarz, W.J. / Schindelin, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural and biochemical studies of the C-terminal domain of mouse peptide-N-glycanase identify it as a mannose-binding module.
Authors: Zhou, X. / Zhao, G. / Truglio, J.J. / Wang, L. / Li, G. / Lennarz, W.J. / Schindelin, H.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 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

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Assembly

Deposited unit
A: peptide N-glycanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1774
Polymers22,9581
Non-polymers2203
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.760, 40.760, 193.663
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-101-

CL

21A-1-

HOH

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Components

#1: Protein peptide N-glycanase / PNGase


Mass: 22957.562 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngly1 / Plasmid: pTXB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: GenBank: 30517852, UniProt: Q9JI78*PLUS, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 14-16% PEG 8000, 100 mM Tris-HCl, pH 8.5, 120 mM MgCl2 and 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.0055 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2004
RadiationMonochromator: Channel cut Si (111) / Protocol: SIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0055 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 15560 / Num. obs: 15560 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 36.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 3.5 / Num. unique all: 765 / Rsym value: 0.622 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.882 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21265 14827 5 %RANDOM
Rwork0.1668 ---
all0.16895 15560 --
obs0.16895 15560 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.135 Å0.139 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 13 98 1577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221514
X-RAY DIFFRACTIONr_bond_other_d0.0020.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9312036
X-RAY DIFFRACTIONr_angle_other_deg1.19433100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76723.95181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55315273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9341513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined0.1940.2237
X-RAY DIFFRACTIONr_nbd_other0.1970.21375
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2732
X-RAY DIFFRACTIONr_nbtor_other0.0820.2950
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.28
X-RAY DIFFRACTIONr_mcbond_it1.0811.51162
X-RAY DIFFRACTIONr_mcbond_other0.2161.5373
X-RAY DIFFRACTIONr_mcangle_it1.28621432
X-RAY DIFFRACTIONr_scbond_it2.3013750
X-RAY DIFFRACTIONr_scangle_it3.2324.5604
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 58 -
Rwork0.188 1058 -
obs--97.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
126.11179.2852-10.304910.4793-3.79938.26480.03071.5556-0.0488-1.7482-0.12510.20550.5494-0.34290.09440.37660.13750.14590.31410.0091-0.34620.19819.80874.3342
24.5578-1.0693-1.81541.97160.74184.5590.18750.75070.3466-0.6318-0.04990.0504-0.3451-0.1686-0.13760.0182-0.001-0.0192-0.07330.0722-0.14529.951716.135814.7683
33.08330.0943-0.44655.6553-1.07233.3569-0.02090.3788-0.1491-0.53450.0620.31670.0793-0.1243-0.0411-0.1461-0.0284-0.0683-0.2324-0.0027-0.23069.37817.475321.0233
44.44920.0293-2.09552.5654-1.88494.2138-0.06410.56520.0832-0.4955-0.0194-0.30620.36620.28790.0834-0.0772-0.02170.0502-0.1076-0.0427-0.16621.920410.225219.5277
520.2763-6.8999-11.15552.39134.731926.3651-0.6560.3856-0.9164-0.07850.10130.28582.21430.54620.5548-0.06620.01590.055-0.2042-0.0472-0.134120.55214.316223.4944
63.2503-0.602-1.49157.45723.424210.0211-0.08150.5021-0.2882-0.3422-0.1208-0.48730.72680.7970.2023-0.09110.06030.0824-0.0407-0.0093-0.077227.50357.970620.5119
732.71273.5422-35.931.6648-6.321344.0753-0.33780.2068-0.6796-0.4783-0.1942-0.11520.70850.72550.532-0.0579-0.02990.0006-0.1789-0.069-0.236317.59315.083720.2882
810.9379-5.02050.852213.3533-4.286.5419-0.1082-0.5905-0.24890.27240.52811.0832-0.1753-0.6819-0.4199-0.20080.00750.0103-0.22840.0201-0.10533.77355.821433.9342
96.98-1.84-0.68310.8895-2.53386.85520.11070.64110.8584-0.42830.055-0.3624-0.7924-0.0195-0.1657-0.0758-0.0034-0.0013-0.22780.0287-0.11439.700919.318624.7685
1029.2643-11.9105-14.20648.44225.921212.85220.09381.682-0.5726-1.0187-0.5043-0.24350.27520.34330.41050.17710.07550.20970.21480.0149-0.11827.744511.784410.5651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA472 - 49022 - 40
2X-RAY DIFFRACTION2AA491 - 53341 - 83
3X-RAY DIFFRACTION3AA534 - 55384 - 103
4X-RAY DIFFRACTION4AA554 - 578104 - 128
5X-RAY DIFFRACTION5AA579 - 583129 - 133
6X-RAY DIFFRACTION6AA584 - 608134 - 158
7X-RAY DIFFRACTION7AA609 - 615159 - 165
8X-RAY DIFFRACTION8AA616 - 624166 - 174
9X-RAY DIFFRACTION9AA625 - 641175 - 191
10X-RAY DIFFRACTION10AA642 - 651192 - 201

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