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- PDB-6u11: Xenopus laevis N-acetylglucosamine-1-phosphodiester alpha-N-acety... -

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Basic information

Entry
Database: PDB / ID: 6u11
TitleXenopus laevis N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) (C46S C219S C453S C480S C486S) with CTD mostly flexible
ComponentsEGF-like domain-containing protein
KeywordsHYDROLASE / uncovering enzyme / mannose 6-phosphate / glycosidase / N-acetylglucosamine
Function / homologyPhosphodiester glycosidase / Phosphodiester glycosidase / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / : / N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionAug 15, 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: Advisory / Atomic model ...Advisory / 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_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn_type.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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EGF-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,91015
Polymers54,2641
Non-polymers1,64614
Water2,540141
1
A: EGF-like domain-containing protein
hetero molecules

A: EGF-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,82130
Polymers108,5282
Non-polymers3,29228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10620 Å2
ΔGint16 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.019, 383.969, 96.767
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-737-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein EGF-like domain-containing protein


Mass: 54264.148 Da / Num. of mol.: 1 / Mutation: C96S, I191M, C269S, L301I, C503S, C530S, C536S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18011890mg / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1L8HDP6

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Sugars , 3 types, 3 molecules

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


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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


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

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Non-polymers , 2 types, 152 molecules

#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 5.74 Å3/Da / Density % sol: 78.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: potassium formate, tris pH 8

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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: 2.7→42.45 Å / Num. obs: 36872 / % possible obs: 71.47 % / Redundancy: 2.9 % / Biso Wilson estimate: 41.41 Å2 / CC1/2: 0.97 / Rrim(I) all: 0.204 / Net I/σ(I): 5.92
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2430 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PKG

6pkg


Resolution: 2.7→42.45 Å / SU ML: 0.2856 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6597
RfactorNum. reflection% reflection
Rfree0.2249 2698 7.34 %
Rwork0.1964 --
obs0.1985 36760 55.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 91 141 2683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292595
X-RAY DIFFRACTIONf_angle_d0.56853529
X-RAY DIFFRACTIONf_chiral_restr0.0421395
X-RAY DIFFRACTIONf_plane_restr0.0045462
X-RAY DIFFRACTIONf_dihedral_angle_d10.63461519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.3233480.264660X-RAY DIFFRACTION20.38
2.75-2.810.2463630.2493784X-RAY DIFFRACTION24.26
2.81-2.860.2763740.2431861X-RAY DIFFRACTION26.98
2.86-2.920.2693800.24671014X-RAY DIFFRACTION31.47
2.92-2.990.2941820.23921120X-RAY DIFFRACTION35.05
2.99-3.070.27711030.22571353X-RAY DIFFRACTION41.53
3.07-3.150.27921080.23981422X-RAY DIFFRACTION44.35
3.15-3.240.23211360.23671673X-RAY DIFFRACTION51.77
3.24-3.350.22841440.20951903X-RAY DIFFRACTION58.96
3.35-3.470.2812950.27711197X-RAY DIFFRACTION37.23
3.47-3.610.23141670.21982011X-RAY DIFFRACTION62.95
3.61-3.770.3276920.23851068X-RAY DIFFRACTION33.38
3.77-3.970.2459930.21071096X-RAY DIFFRACTION34.13
3.97-4.220.21022100.14552876X-RAY DIFFRACTION88.5
4.22-4.540.15022270.13382884X-RAY DIFFRACTION89.47
4.54-50.16412320.13552957X-RAY DIFFRACTION92.46
5-5.720.19682510.17063143X-RAY DIFFRACTION97.08
5.72-7.20.2592490.2193021X-RAY DIFFRACTION94.35
7.2-42.450.25062440.24843019X-RAY DIFFRACTION93.5

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