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- PDB-6pku: Guinea pig N-acetylglucosamine-1-phosphodiester alpha-N-acetylglu... -

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Basic information

Entry
Database: PDB / ID: 6pku
TitleGuinea pig N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C51S C221S) in complex with N-acetyl-alpha-D-glucosamine (alpha-GlcNAc) and mannose 6-phosphate (M6P)
ComponentsN-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
KeywordsHYDROLASE / uncovering enzyme / mannose 6-phosphate / glycosidase / N-acetylglucosamine
Function / homologyPhosphodiester glycosidase / Phosphodiester glycosidase / secretion of lysosomal enzymes / membrane / 6-O-phosphono-alpha-D-mannopyranose / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
Function and homology information
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsGorelik, A. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: Structure / Year: 2020
Title: Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme.
Authors: Gorelik, A. / Illes, K. / Nagar, B.
History
DepositionJun 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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

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Assembly

Deposited unit
A: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
B: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
C: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
D: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,11913
Polymers129,9734
Non-polymers2,1479
Water11,836657
1
A: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
C: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9496
Polymers64,9862
Non-polymers9634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-15 kcal/mol
Surface area19930 Å2
MethodPISA
2
B: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
D: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1707
Polymers64,9862
Non-polymers1,1845
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-9 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.459, 232.556, 65.305
Angle α, β, γ (deg.)90.00, 109.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)


Mass: 32493.127 Da / Num. of mol.: 4 / Mutation: C67S, C237S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: NAGPA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: H0VTT5
#2: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-M6P / 6-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-mannose / 6-O-phosphono-D-mannose / 6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Manp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 10 mM tri-sodium citrate, 16% PEG 6000, soaked in 50 mM N-acetylglucosamine and 50 mM mannose 6-phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.949→50 Å / Num. obs: 149942 / % possible obs: 99.1 % / Redundancy: 6 % / Net I/σ(I): 13.1
Reflection shellResolution: 1.949→2.02 Å / Num. unique obs: 8692

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PKG

6pkg


Resolution: 1.949→30.779 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9
RfactorNum. reflection% reflection
Rfree0.2324 3507 2.34 %
Rwork0.2012 --
obs0.2019 149942 84.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.949→30.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8007 0 138 657 8802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068306
X-RAY DIFFRACTIONf_angle_d0.81911275
X-RAY DIFFRACTIONf_dihedral_angle_d11.3394904
X-RAY DIFFRACTIONf_chiral_restr0.0471250
X-RAY DIFFRACTIONf_plane_restr0.0041504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9485-1.97520.2376680.26493268X-RAY DIFFRACTION46
1.9752-2.00340.3011280.25015283X-RAY DIFFRACTION78
2.0034-2.03330.33651460.24936167X-RAY DIFFRACTION89
2.0333-2.06510.3315420.24221425X-RAY DIFFRACTION92
2.0651-2.09890.4047780.31293065X-RAY DIFFRACTION82
2.0989-2.13510.25341620.21456785X-RAY DIFFRACTION99
2.1351-2.17390.24561740.2046979X-RAY DIFFRACTION99
2.1739-2.21570.21961360.20675774X-RAY DIFFRACTION100
2.261-2.31010.29391380.22475564X-RAY DIFFRACTION99
2.3101-2.36380.23991680.19466823X-RAY DIFFRACTION100
2.3638-2.42290.21711710.19127084X-RAY DIFFRACTION100
2.4229-2.48840.23631570.19776704X-RAY DIFFRACTION100
2.4884-2.56160.21271620.20046999X-RAY DIFFRACTION100
2.5616-2.64420.31711680.20926819X-RAY DIFFRACTION100
2.6442-2.73870.26661680.21176962X-RAY DIFFRACTION100
2.7387-2.84820.24671600.19656859X-RAY DIFFRACTION100
2.8482-2.97780.22871660.20416861X-RAY DIFFRACTION100
2.9778-3.13460.22061720.19356911X-RAY DIFFRACTION100
3.1346-3.33080.24651720.18856856X-RAY DIFFRACTION100
3.3308-3.58760.21871580.18436851X-RAY DIFFRACTION99
3.5876-3.9480.19161580.1866631X-RAY DIFFRACTION96
3.948-4.51770.19421560.18046511X-RAY DIFFRACTION95
4.5177-5.6860.19841500.1896488X-RAY DIFFRACTION94
5.686-30.78280.24261490.23216766X-RAY DIFFRACTION98

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