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

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Basic information

Entry
Database: PDB / ID: 6pkh
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 / anatomical structure development / 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
N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _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 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5292
Polymers35,6341
Non-polymers8951
Water7,692427
1
A: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
hetero molecules

A: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0574
Polymers71,2672
Non-polymers1,7902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4330 Å2
ΔGint17 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.954, 73.954, 109.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

21A-922-

HOH

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Components

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


Mass: 35633.746 Da / Num. of mol.: 1
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
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 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-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, HEPES pH 7.5, cryo-protected with sodium malonate

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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: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 38530 / % possible obs: 93.8 % / Redundancy: 15.3 % / Net I/σ(I): 47.6
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 2264

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PKG

6pkg


Resolution: 1.6→35.026 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.41
RfactorNum. reflection% reflection
Rfree0.1726 2904 5.54 %
Rwork0.138 --
obs0.1399 52393 68.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→35.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 60 427 2861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072517
X-RAY DIFFRACTIONf_angle_d0.9153435
X-RAY DIFFRACTIONf_dihedral_angle_d10.211506
X-RAY DIFFRACTIONf_chiral_restr0.054395
X-RAY DIFFRACTIONf_plane_restr0.006444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62630.3208320.3042537X-RAY DIFFRACTION16
1.6263-1.65430.2796440.2731748X-RAY DIFFRACTION22
1.6543-1.68440.2308550.256945X-RAY DIFFRACTION27
1.6844-1.71680.234660.21441107X-RAY DIFFRACTION32
1.7168-1.75180.2219790.21231332X-RAY DIFFRACTION39
1.7518-1.78990.1887860.18881479X-RAY DIFFRACTION43
1.7899-1.83150.2084920.1811622X-RAY DIFFRACTION47
1.8315-1.87730.19631090.17481846X-RAY DIFFRACTION54
1.8773-1.92810.22281220.19172106X-RAY DIFFRACTION61
1.9281-1.98480.19571390.16672333X-RAY DIFFRACTION68
1.9848-2.04890.17011580.14782619X-RAY DIFFRACTION76
2.0489-2.12210.19331670.13882877X-RAY DIFFRACTION84
2.1221-2.20710.21091780.13633120X-RAY DIFFRACTION91
2.2071-2.30750.17511930.14773193X-RAY DIFFRACTION93
2.3075-2.42910.1791970.13283369X-RAY DIFFRACTION98
2.4291-2.58130.18072010.1383387X-RAY DIFFRACTION98
2.5813-2.78050.18891980.13613351X-RAY DIFFRACTION98
2.7805-3.06020.18092000.12713401X-RAY DIFFRACTION98
3.0602-3.50260.16141950.11533346X-RAY DIFFRACTION97
3.5026-4.41160.11811950.10513364X-RAY DIFFRACTION98
4.4116-35.03480.16021980.143407X-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)
10.2152-0.1260.07760.40030.14440.21660.15680.2973-0.0413-0.1592-0.1320.08380.0219-0.03760.00560.11720.017-0.01190.16680.00440.09616.577244.02738.7585
20.12260.26290.03240.6699-0.06590.5517-0.0193-0.15820.12420.2030.10890.0538-0.0602-0.06810.46140.1380.04660.01050.1589-0.04650.093611.050857.272259.2184
31.0543-0.2227-0.16520.8946-0.56320.6473-0.0777-0.1819-0.1936-0.08890.01470.1648-0.0188-0.2465-0.05080.11160.0047-0.02470.16430.0150.13522.564433.678360.4892
40.8519-0.3925-0.30230.9318-0.11920.7458-0.01120.01670.14440.0258-0.0095-0.127-0.06920.0022-0.00020.0908-0.0107-0.00190.09850.00670.131329.896952.079246.1475
50.2458-0.36520.18280.9088-0.48060.63150.0273-0.02280.3290.0923-0.0267-0.0348-0.1303-0.07820.00160.0887-0.00050.00850.0920.00040.147219.716559.96750.7282
60.6635-0.16640.07310.41260.23820.3767-0.0216-0.10170.31240.11830.08660.0314-0.1655-0.03450.0130.09690.02010.01920.07090.0040.121514.077757.759353.6012
70.6634-0.3926-0.34151.2321-0.20490.34060.0032-0.044-0.08340.02590.02260.22160.0121-0.14430.03470.06710.0116-0.00140.10250.00660.083612.660743.748651.3557
80.793-0.27190.27020.70740.10470.2663-0.0274-0.0813-0.13720.10330.03270.05640.0392-0.01280.01550.09310.00740.00580.09780.02230.067917.36338.905355.3999
90.3198-0.34830.09840.427-0.13240.0427-0.0080.12430.0686-0.00230.008-0.06010.06920.1126-0.00120.10180.0104-0.0150.10820.00680.107833.548937.044747.2559
100.562-0.0854-0.22550.2969-0.41130.7732-0.0477-0.03520.10880.06790.0747-0.17290.01260.1829-0.00960.09090.022-0.02360.1008-0.0020.119132.191144.609348.6782
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 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 190 )
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 221 )
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 265 )
8X-RAY DIFFRACTION8chain 'A' and (resid 266 through 299 )
9X-RAY DIFFRACTION9chain 'A' and (resid 300 through 319 )
10X-RAY DIFFRACTION10chain 'A' and (resid 320 through 336 )

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