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- PDB-2g9g: Crystal structure of His-tagged mouse PNGase C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2g9g
TitleCrystal structure of His-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 / collagen-containing extracellular matrix / nucleus / metal ion binding / cytosol / cytoplasm
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 ...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 / MOLECULAR REPLACEMENT / Resolution: 2 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 / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)25,6016
Polymers25,1291
Non-polymers4725
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: peptide N-glycanase
hetero molecules

A: peptide N-glycanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,20312
Polymers50,2582
Non-polymers94510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area3110 Å2
ΔGint-91 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.732, 40.747, 66.506
Angle α, β, γ (deg.)90.00, 95.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-125-

SO4

21A-2-

HOH

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Components

#1: Protein peptide N-glycanase / PNGase


Mass: 25128.934 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: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Condon Plus RIL
References: GenBank: 30517852, UniProt: Q9JI78*PLUS, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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.: 115 / 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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6 M Li2SO4 and 100 mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9996 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2004
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9996 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 13124 / Num. obs: 13124 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1311 / Rsym value: 0.485 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2G2F

2g2f


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.7 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20711 646 4.9 %RANDOM
Rwork0.15028 ---
all0.15304 13124 --
obs0.15304 12453 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.07 Å2
2---0.3 Å20 Å2
3---0.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.155 Å0.166 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 27 115 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211595
X-RAY DIFFRACTIONr_bond_other_d0.0010.021405
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9372146
X-RAY DIFFRACTIONr_angle_other_deg0.83933258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43923.49483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34415283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3931515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined0.1770.2239
X-RAY DIFFRACTIONr_nbd_other0.1890.21468
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2745
X-RAY DIFFRACTIONr_nbtor_other0.0820.2975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0220.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.213
X-RAY DIFFRACTIONr_mcbond_it2.81121212
X-RAY DIFFRACTIONr_mcbond_other0.7612393
X-RAY DIFFRACTIONr_mcangle_it3.31531496
X-RAY DIFFRACTIONr_scbond_it4.9174800
X-RAY DIFFRACTIONr_scangle_it6.5025650
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 51 -
Rwork0.174 904 -
obs--97.25 %
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)
110.71135.71190.575415.14692.22525.3130.1046-0.9617-0.08280.8512-0.19490.48330.2808-0.32210.0903-0.01930.01140.06750.06860.0049-0.2438-24.77271.51-3.0199
22.0011-0.90830.06228.1293.79425.6694-0.1069-0.5165-0.02840.57970.2769-0.358-0.14090.5028-0.1701-0.09540.0052-0.0378-0.0111-0.0133-0.1653-13.0931-0.0494-11.6139
313.3825-0.92363.77331.50490.45523.9977-0.2448-0.5033-0.41690.46360.1710.41610.1501-0.29830.0738-0.046-0.00630.0437-0.09560.0639-0.1912-24.1648-6.5119-12.8551
41.5887-0.8387-0.45551.47040.73421.7657-0.056-0.1808-0.12770.10720.10270.08160.10710.0165-0.0467-0.1395-0.0002-0.0075-0.1760.033-0.1149-21.481-10.8431-23.6808
51.427-0.1898-0.97433.28442.10743.25430.135-0.27770.17760.3994-0.0334-0.0134-0.184-0.0415-0.1016-0.04580.0040.0217-0.1184-0.0293-0.1446-21.98537.9421-16.7342
60.95551.59661.9572.80123.15544.10610.15630.20660.1275-0.0882-0.0102-0.1308-0.1978-0.1338-0.1461-0.13030.00060.0055-0.18050.0243-0.1228-26.2466-1.4261-31.1014
73.79480.4625-1.51772.35790.3353.92160.0734-0.03990.43260.2178-0.03180.2192-0.353-0.3064-0.0415-0.1190.03970.0045-0.177-0.0301-0.09-24.959310.7369-21.3597
81.9567-0.13841.66961.28452.36236.2512-0.0424-0.04330.1411-0.2302-0.0110.1688-0.3589-0.10080.0534-0.1941-0.00850.0371-0.16880.0228-0.112-28.2126-0.8139-25.0776
93.5524-0.55911.36323.53750.20562.07630.1276-0.0462-0.10350.04210.0003-0.210.19720.1486-0.1278-0.1920.01440.0069-0.18950.0005-0.1473-16.4715-9.2389-27.8492
103.8457-6.3822-5.098815.567611.05668.9106-0.1858-0.19310.11480.7675-0.10130.66960.0154-0.08430.28710.00220.04120.0224-0.0547-0.0966-0.1393-20.416911.4854-11.6102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA454 - 48824 - 58
2X-RAY DIFFRACTION2AA489 - 50959 - 79
3X-RAY DIFFRACTION3AA510 - 52280 - 92
4X-RAY DIFFRACTION4AA523 - 55293 - 122
5X-RAY DIFFRACTION5AA553 - 573123 - 143
6X-RAY DIFFRACTION6AA574 - 581144 - 151
7X-RAY DIFFRACTION7AA582 - 608152 - 178
8X-RAY DIFFRACTION8AA609 - 618179 - 188
9X-RAY DIFFRACTION9AA619 - 641189 - 211
10X-RAY DIFFRACTION10AA642 - 651212 - 221

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