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- PDB-6pkg: Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylgluc... -

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Basic information

Entry
Database: PDB / ID: 6pkg
TitleZebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide
ComponentsN-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
KeywordsHYDROLASE / uncovering enzyme / mannose 6-phosphate / glycosidase / pro-peptide
Function / homology
Function and homology information


secretion of lysosomal enzymes / membrane
Similarity search - Function
Phosphodiester glycosidase / Phosphodiester glycosidase / Laminin-type EGF domain / EGF-like domain, extracellular / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
molecular iodine / IODIDE ION / N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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_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_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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
B: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,16970
Polymers71,2672
Non-polymers11,90168
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-6 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.356, 124.356, 278.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase


Mass: 35633.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: nagpa / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1QSF9

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

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Non-polymers , 4 types, 321 molecules

#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-I2I / molecular iodine


Mass: 253.809 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I2
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 7.56 Å3/Da / Density % sol: 83.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 50% PEG 200, 0.1M HEPES pH 6.4, soaked in 1M NaI

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 90810 / % possible obs: 98.9 % / Redundancy: 20 % / Net I/σ(I): 16.1
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 4913

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→35.658 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1
RfactorNum. reflection% reflection
Rfree0.2081 3478 3.83 %
Rwork0.1831 --
obs0.184 90810 88.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→35.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4748 0 210 257 5215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034998
X-RAY DIFFRACTIONf_angle_d0.5426755
X-RAY DIFFRACTIONf_dihedral_angle_d11.1592958
X-RAY DIFFRACTIONf_chiral_restr0.044766
X-RAY DIFFRACTIONf_plane_restr0.002881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.83840.3138570.32571491X-RAY DIFFRACTION37
2.8384-2.87890.3118660.29991591X-RAY DIFFRACTION41
2.8789-2.92190.3484750.27481816X-RAY DIFFRACTION46
2.9219-2.96750.3085870.29072143X-RAY DIFFRACTION54
2.9675-3.01610.3129970.28582445X-RAY DIFFRACTION62
3.0161-3.06810.31571270.27933109X-RAY DIFFRACTION79
3.0681-3.12390.26031440.28943749X-RAY DIFFRACTION93
3.1239-3.18390.28791570.27833859X-RAY DIFFRACTION98
3.1839-3.24890.28161570.25843947X-RAY DIFFRACTION100
3.2489-3.31950.27591570.22133939X-RAY DIFFRACTION100
3.3195-3.39660.21841630.20523969X-RAY DIFFRACTION100
3.3966-3.48150.20051500.19113937X-RAY DIFFRACTION100
3.4815-3.57560.19041530.17523948X-RAY DIFFRACTION100
3.5756-3.68070.20961610.17233963X-RAY DIFFRACTION100
3.6807-3.79930.22311570.1533941X-RAY DIFFRACTION100
3.7993-3.9350.18111560.14363946X-RAY DIFFRACTION100
3.935-4.09230.1411530.12433975X-RAY DIFFRACTION100
4.0923-4.27830.12811580.11823962X-RAY DIFFRACTION100
4.2783-4.50340.12231540.11743925X-RAY DIFFRACTION100
4.5034-4.78490.1531620.11533951X-RAY DIFFRACTION100
4.7849-5.15340.15681550.13873947X-RAY DIFFRACTION100
5.1534-5.67010.1851540.15693959X-RAY DIFFRACTION100
5.6701-6.48630.25771610.20013950X-RAY DIFFRACTION100
6.4863-8.15590.25111590.21053932X-RAY DIFFRACTION100
8.1559-35.6580.25311580.24443938X-RAY DIFFRACTION99
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)
13.7568-2.6233-4.01712.64830.83686.30020.03660.31030.2296-0.2440.04730.12820.1306-0.795-0.03740.5214-0.156-0.12270.5196-0.02620.368869.111324.595768.8586
23.64541.3782-0.27384.3012-2.46523.261-0.1857-0.2524-0.74560.1398-0.1925-0.31220.87950.90570.42980.62040.15560.08260.29160.05880.543890.569615.59778.0935
33.4589-0.3960.06634.16463.31473.16880.08990.16120.6042-0.1675-0.2196-0.7983-0.44850.17740.25260.2982-0.11530.05790.3369-0.00960.471874.339529.703492.4183
42.57270.2273-0.86151.5494-0.48942.6052-0.20170.2804-0.5774-0.46890.02360.1190.8371-0.32720.17630.6405-0.10610.01250.2863-0.04320.525672.22210.097477.1729
52.64830.9752-0.05434.57980.33893.3110.04660.2958-0.3861-0.599-0.0516-0.48580.55750.0712-0.01320.42150.00170.08630.2623-0.0140.332384.482118.474672.2364
63.9784-1.32490.24744.367-0.24552.3426-0.08850.07610.1109-0.1020.00220.01520.0633-0.10.050.2608-0.11220.03330.22550.01860.246677.016326.743182.8424
73.2097-1.0729-1.26577.26011.60184.37050.003-0.0234-0.1393-0.39640.02270.18260.7033-0.832-0.03260.4118-0.227-0.0190.41130.01330.332461.945418.636185.3632
83.5705-3.352-4.13434.17462.96466.1729-0.2119-0.91680.33790.38870.456-0.23560.16780.5748-0.36060.4715-0.0598-0.00390.6171-0.04070.4558.980833.5422117.0203
91.6563-0.4629-0.0041.6977-0.61221.6477-0.06680.5173-0.1101-0.13960.12250.36630.0488-1.13260.01440.3539-0.20770.04210.80290.13450.599935.301931.1863109.8639
104.86852.3225-2.90572.5794-3.58544.97480.18950.11410.28870.07240.05390.2812-0.2592-0.612-0.17570.322-0.07140.02850.46820.07620.435754.316833.74692.7596
114.64760.75570.42364.4290.80553.12920.2734-0.3858-0.77560.5763-0.0748-0.10780.7278-0.1178-0.22070.5093-0.15870.08710.44470.15640.460751.96415.4834111.5102
122.472-2.1562-1.65813.88651.45535.1494-0.1322-0.2652-0.30760.46230.15350.02170.55880.21540.03920.3629-0.1558-0.01040.40260.08490.441156.531919.7748111.141
132.74870.80721.39223.0830.29212.1349-0.0591-0.5892-0.32430.1688-0.05890.17530.3748-0.59490.16190.3684-0.14670.07280.60640.1160.401640.442122.8283116.4741
146.7166-1.76240.24337.7023-3.10566.14650.1044-0.66210.84260.65260.2210.1446-0.7726-0.6259-0.39120.2805-0.05990.12070.43670.02930.410245.15440.3823112.4393
155.82282.7685-1.06584.61950.35273.2201-0.13720.3190.4017-0.21290.2541-0.073-0.0315-0.193-0.1190.2754-0.0708-0.01370.28450.07010.333853.256834.728103.4023
165.6774-1.0581-1.78232.50660.49243.78170.01540.2390.0467-0.07690.03870.020.0585-0.2335-0.07830.2842-0.1233-0.01380.30180.07490.238155.770129.3626101.2312
175.0898-1.2383-1.09182.2327-0.41055.28070.15090.008-0.48110.2938-0.1418-0.06910.44540.1618-0.02550.3775-0.0886-0.02540.25570.04590.306559.076719.7238104.7667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 190 )
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 235 )
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 299 )
7X-RAY DIFFRACTION7chain 'A' and (resid 300 through 336 )
8X-RAY DIFFRACTION8chain 'B' and (resid 30 through 49 )
9X-RAY DIFFRACTION9chain 'B' and (resid 50 through 79 )
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 106 )
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 131 )
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 160 )
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 209 )
14X-RAY DIFFRACTION14chain 'B' and (resid 210 through 235 )
15X-RAY DIFFRACTION15chain 'B' and (resid 236 through 275 )
16X-RAY DIFFRACTION16chain 'B' and (resid 276 through 319 )
17X-RAY DIFFRACTION17chain 'B' and (resid 320 through 336 )

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