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- PDB-2ffu: Crystal Structure of Human ppGalNAcT-2 complexed with UDP and EA2 -

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Basic information

Entry
Database: PDB / ID: 2ffu
TitleCrystal Structure of Human ppGalNAcT-2 complexed with UDP and EA2
Components
  • 13-Peptide EA2, PTTDSTTPAPTTK
  • Polypeptide N-acetylgalactosaminyltransferase 2
KeywordsTRANSFERASE / ppGalNAcT / mucin / glycosyltransferase
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 / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane ...protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane / protein maturation / manganese ion binding / carbohydrate binding / Golgi membrane / nucleotide binding / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / : / Polypeptide N-acetylgalactosaminyltransferase 2 / Submandibular gland mucin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFritz, T.A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Dynamic Association between the Catalytic and Lectin Domains of Human UDP-GalNAc:Polypeptide {alpha}-N-Acetylgalactosaminyltransferase-2
Authors: Fritz, T.A. / Raman, J. / Tabak, L.A.
History
DepositionDec 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polypeptide N-acetylgalactosaminyltransferase 2
P: 13-Peptide EA2, PTTDSTTPAPTTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9074
Polymers58,4482
Non-polymers4592
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-30 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.344, 69.344, 169.124
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe biological unit is a monomer

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Components

#1: Protein Polypeptide N-acetylgalactosaminyltransferase 2 / E.C.2.4.1.41 / ppGalNAcT-2 / Protein-UDP acetylgalactosaminyltransferase 2 / UDP-GalNAc:polypeptide N- ...ppGalNAcT-2 / Protein-UDP acetylgalactosaminyltransferase 2 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2 / Polypeptide GalNAc transferase 2 / GalNAc-T2 / pp-GaNTase 2


Mass: 57129.844 Da / Num. of mol.: 1 / Fragment: Catalytic and lectin domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Invitrogen pPIC9 vector with TEV-protease-cleavable, N-terminal engineered 6His tag
Gene: GALNT2 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide 13-Peptide EA2, PTTDSTTPAPTTK


Mass: 1318.406 Da / Num. of mol.: 1 / Fragment: residues 244-256 of rat submandibular gland mucin / Source method: obtained synthetically / Details: occurs naturally in Rattus norvegicus / References: GenBank: 995765, UniProt: Q63549*PLUS
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, Hepes, mercaptoethanol, UDP, EDTA, MnCl2, EA2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→24.48 Å / Num. all: 56123 / Num. obs: 55904 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.9 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→24.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2043107.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2822 5 %RANDOM
Rwork0.178 ---
all0.179 56123 --
obs0.179 55904 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.1702 Å2 / ksol: 0.39239 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.84 Å20 Å2
2---0.21 Å20 Å2
3---0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.64→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4022 0 26 495 4543
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it2.742
X-RAY DIFFRACTIONc_scangle_it4.292.5
LS refinement shellResolution: 1.64→1.74 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 468 5 %
Rwork0.215 8825 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramudp.topo2
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4udp.param2ion.top

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