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- PDB-2i74: Crystal structure of mouse Peptide N-Glycanase C-terminal domain ... -

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Basic information

Entry
Database: PDB / ID: 2i74
TitleCrystal structure of mouse Peptide N-Glycanase C-terminal domain in complex with mannopentaose
ComponentsPNGase
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 domain / PUB-like domain superfamily / 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 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 / Papain-like cysteine peptidase superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionAug 30, 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 1.3Oct 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PNGase
B: PNGase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,93513
Polymers43,9712
Non-polymers1,96411
Water5,783321
1
A: PNGase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0137
Polymers21,9851
Non-polymers1,0286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PNGase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9216
Polymers21,9851
Non-polymers9365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.706, 41.646, 94.900
Angle α, β, γ (deg.)90.000, 94.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PNGase / Peptide N-glycanase


Mass: 21985.439 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 471-651
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngly1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Condon Plus RIL
References: UniProt: Q9JI78, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122h-1a_1-5]/1-1-1-1/a6-b1_b3-c1_b6-d1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19 % PEG 4000, 11.5 % Isopropanol, 0.1 M Tris-HCl, pH 7.5, 0.2 M Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2006
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 35889 / Num. obs: 35889 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Χ2: 0.995 / Net I/σ(I): 20
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3565 / Rsym value: 0.441 / Χ2: 0.759 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G9F

2g9f


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.701 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1856 5.2 %RANDOM
Rwork0.172 ---
all0.174 35889 --
obs-35851 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.838 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20.44 Å2
2---0.59 Å20 Å2
3----0.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.117 Å0.125 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 132 321 3368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213106
X-RAY DIFFRACTIONr_bond_other_d0.0010.022132
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.974185
X-RAY DIFFRACTIONr_angle_other_deg1.66835129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55324.088159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52615536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1861525
X-RAY DIFFRACTIONr_chiral_restr0.1250.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023371
X-RAY DIFFRACTIONr_gen_planes_other00.02654
X-RAY DIFFRACTIONr_nbd_refined0.2150.3520
X-RAY DIFFRACTIONr_nbd_other0.2340.32277
X-RAY DIFFRACTIONr_nbtor_refined0.1810.51488
X-RAY DIFFRACTIONr_nbtor_other0.0940.51701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.5447
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4010.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3460.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.541
X-RAY DIFFRACTIONr_mcbond_it1.1271.52337
X-RAY DIFFRACTIONr_mcbond_other0.2511.5743
X-RAY DIFFRACTIONr_mcangle_it1.29422864
X-RAY DIFFRACTIONr_scbond_it2.30931557
X-RAY DIFFRACTIONr_scangle_it3.244.51321
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 128 -
Rwork0.21 2401 -
obs-2529 96.9 %
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)
11.07510.2093-0.54661.648-0.28151.4257-0.0429-0.01910.0059-0.06640.07470.2070.0871-0.0811-0.0317-0.054-0.0013-0.008-0.02820.0132-0.032313.32270.349938.1889
20.956-0.09410.43180.946-0.19520.9223-0.0168-0.01430.00050.06270.02260.0574-0.08-0.011-0.0058-0.05440.00090.0068-0.0649-0.0007-0.06715.849214.32497.897
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 472 - 651 / Label seq-ID: 2 - 181

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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