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- PDB-3esw: Complex of yeast PNGase with GlcNAc2-IAc. -

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Basic information

Entry
Database: PDB / ID: 3esw
TitleComplex of yeast PNGase with GlcNAc2-IAc.
Components
  • Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
  • UV excision repair protein RAD23
KeywordsHYDROLASE / Glycoproteins Peptide:N-glycanase Chitobiose / Metal-binding / Nucleus / DNA damage / DNA repair / Phosphoprotein / Ubl conjugation pathway
Function / homology
Function and homology information


ubiquitin-dependent glycoprotein ERAD pathway / PNGase complex / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / nucleotide-excision repair factor 2 complex / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / nucleotide-excision repair, DNA damage recognition / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding ...ubiquitin-dependent glycoprotein ERAD pathway / PNGase complex / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / nucleotide-excision repair factor 2 complex / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / nucleotide-excision repair, DNA damage recognition / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding / ERAD pathway / ubiquitin binding / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XPC-binding domain / C8orf32 fold - #30 / C8orf32 fold / : / Rad4 transglutaminase-like domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Transglutaminase-like superfamily ...XPC-binding domain / C8orf32 fold - #30 / C8orf32 fold / : / Rad4 transglutaminase-like domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Transglutaminase-like superfamily / Heat shock chaperonin-binding / Transglutaminase/protease-like homologues / Heat shock chaperonin-binding motif. / Transglutaminase-like / UBA/TS-N domain / N-terminal domain of TfIIb - #10 / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / N-terminal domain of TfIIb / UBA-like superfamily / Single Sheet / Papain-like cysteine peptidase superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UV excision repair protein RAD23 / Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsZhao, G. / Zhou, X. / Lennarz, W.J. / Schindelin, H.
CitationJournal: Glycobiology / Year: 2009
Title: Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase.
Authors: Zhao, G. / Li, G. / Zhou, X. / Matsuo, I. / Ito, Y. / Suzuki, T. / Lennarz, W.J. / Schindelin, H.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 2.1Sep 6, 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: Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
B: UV excision repair protein RAD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2384
Polymers47,7482
Non-polymers4902
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-8 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.530, 131.530, 127.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase / PNGase / Peptide:N-glycanase 1 / yPNG1


Mass: 41698.070 Da / Num. of mol.: 1 / Fragment: peptide:N-glycanase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PNG1, YPL096W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Codon Plus RIL
References: UniProt: Q02890, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Protein UV excision repair protein RAD23


Mass: 6049.967 Da / Num. of mol.: 1 / Fragment: XPCB Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD23, SYGP-ORF29, YEL037C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Codon Plus RIL / References: UniProt: P32628
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 6.68 Å3/Da / Density % sol: 81.59 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5 and 2.0 M sodium chloride, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→37.969 Å / Num. obs: 17986 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 5.496
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.4 / Num. measured all: 20859 / Num. unique all: 2581 / Rsym value: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: PDB ENTRY 1X3Z

1x3z


Resolution: 3.4→37.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 31.04 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.42 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1084 5 %RANDOM
Rwork0.197 ---
obs0.199 17961 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 106.09 Å2 / Biso mean: 63.61 Å2 / Biso min: 7.26 Å2
Baniso -1Baniso -2Baniso -3
1-6.04 Å23.02 Å20 Å2
2--6.04 Å20 Å2
3----9.05 Å2
Refinement stepCycle: LAST / Resolution: 3.4→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 29 7 3220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223282
X-RAY DIFFRACTIONr_bond_other_d0.0010.022260
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.964431
X-RAY DIFFRACTIONr_angle_other_deg0.95235485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6745384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58924.593172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.01115580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0611520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02672
X-RAY DIFFRACTIONr_mcbond_it0.6191.51930
X-RAY DIFFRACTIONr_mcbond_other0.0671.5778
X-RAY DIFFRACTIONr_mcangle_it1.18323119
X-RAY DIFFRACTIONr_scbond_it1.23631352
X-RAY DIFFRACTIONr_scangle_it2.1574.51312
LS refinement shellResolution: 3.4→3.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 2581 -
Rwork0.349 1468 -
all-1553 -
obs--99.94 %
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)
11.49111.271.00911.77291.00221.108-0.2150.01750.0487-0.10950.0850.1496-0.14930.27090.130.0506-0.03370.01570.22530.02110.052784.874747.402599.4067
24.4614-0.03513.79510.74121.68939.24520.1354-0.27030.0298-0.07830.1641-0.09850.3401-0.4694-0.29950.0994-0.14870.00380.23110.00080.05158.438335.819482.9119
39.20333.0831.43878.95652.57157.3019-0.154-0.51470.5066-0.30660.0341-0.1314-0.24660.73330.120.0235-0.06130.00070.3482-0.03370.0421108.964660.0945106.8493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 123
2X-RAY DIFFRACTION1A190 - 328
3X-RAY DIFFRACTION2A124 - 189
4X-RAY DIFFRACTION3B253 - 309

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