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- PDB-6e7i: Human ppGalNAcT2 I253A/L310A Mutant with EA2 and UDP -

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Basic information

Entry
Database: PDB / ID: 6e7i
TitleHuman ppGalNAcT2 I253A/L310A Mutant with EA2 and UDP
Components
  • EA2
  • Polypeptide N-acetylgalactosaminyltransferase 2
KeywordsTRANSFERASE / glycosyltransferase / glycosylation / bump-hole / galnac
Function / homology
Function and homology information


protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked GalNAcylation / O-linked glycosylation of mucins / regulation of sensory perception of pain / peptidase inhibitor activity / Golgi stack / protein O-linked glycosylation ...protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked GalNAcylation / O-linked glycosylation of mucins / regulation of sensory perception of pain / peptidase inhibitor activity / Golgi stack / protein O-linked glycosylation / COPI-independent Golgi-to-ER retrograde traffic / Golgi cisterna membrane / endopeptidase inhibitor activity / positive regulation of immunoglobulin production / protein maturation / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular region / membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Polypeptide N-acetylgalactosaminyltransferase 2 / Apomucin
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBertozzi, C.R. / Schumann, B. / Agbay, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)NIH R01 CA200423 United States
CitationJournal: Mol.Cell / Year: 2020
Title: Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells.
Authors: Schumann, B. / Malaker, S.A. / Wisnovsky, S.P. / Debets, M.F. / Agbay, A.J. / Fernandez, D. / Wagner, L.J.S. / Lin, L. / Li, Z. / Choi, J. / Fox, D.M. / Peh, J. / Gray, M.A. / Pedram, K. / ...Authors: Schumann, B. / Malaker, S.A. / Wisnovsky, S.P. / Debets, M.F. / Agbay, A.J. / Fernandez, D. / Wagner, L.J.S. / Lin, L. / Li, Z. / Choi, J. / Fox, D.M. / Peh, J. / Gray, M.A. / Pedram, K. / Kohler, J.J. / Mrksich, M. / Bertozzi, C.R.
History
DepositionJul 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polypeptide N-acetylgalactosaminyltransferase 2
P: EA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4484
Polymers61,9892
Non-polymers4592
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-28 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.310, 69.310, 169.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Polypeptide N-acetylgalactosaminyltransferase 2 / Polypeptide GalNAc transferase 2 / pp-GaNTase 2 / Protein-UDP acetylgalactosaminyltransferase 2 / ...Polypeptide GalNAc transferase 2 / pp-GaNTase 2 / Protein-UDP acetylgalactosaminyltransferase 2 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2


Mass: 60670.133 Da / Num. of mol.: 1 / Mutation: I253A,L310A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT2 / Cell line (production host): HEK293 - FreeStyle 293-F / Production host: Homo sapiens (human)
References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide EA2


Mass: 1318.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q62605
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8000, HEPES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 22, 2017
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.8→60.02 Å / Num. obs: 42632 / % possible obs: 92.1 % / Redundancy: 2 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 5.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 0.715 / Num. unique obs: 5819 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FFU

2ffu


Resolution: 1.8→56.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.397 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 1998 5.1 %RANDOM
Rwork0.16719 ---
obs0.1696 37096 91.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.453 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.8→56.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 25 1 327 4308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0144086
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173551
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6645549
X-RAY DIFFRACTIONr_angle_other_deg1.0131.6418334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95421.703229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28215672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3591533
X-RAY DIFFRACTIONr_chiral_restr0.0860.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02764
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5791.6062012
X-RAY DIFFRACTIONr_mcbond_other1.5741.6052011
X-RAY DIFFRACTIONr_mcangle_it2.4432.4012512
X-RAY DIFFRACTIONr_mcangle_other2.4432.4022513
X-RAY DIFFRACTIONr_scbond_it1.9881.7512074
X-RAY DIFFRACTIONr_scbond_other1.9891.7512075
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0412.5563037
X-RAY DIFFRACTIONr_long_range_B_refined4.43618.5854639
X-RAY DIFFRACTIONr_long_range_B_other4.36218.3814576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 142 -
Rwork0.249 2876 -
obs--94.76 %

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