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- PDB-2vxl: Screening a Limited Structure-based Library Identifies UDP-GalNAc... -

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Basic information

Entry
Database: PDB / ID: 2vxl
TitleScreening a Limited Structure-based Library Identifies UDP-GalNAc- Specific Mutants of alpha-1,3 Galactosyltransferase
ComponentsN-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / GALACTOSYLTRANSFERASE / TRANSMEMBRANE / GOLGI APPARATUS / ENZYME MECHANISM / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / ALPHA-1 / MEMBRANE / MANGANESE / TRANSFERASE SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / : / Golgi cisterna membrane / : / glycosyltransferase activity / vesicle / carbohydrate metabolic process / Golgi apparatus / metal ion binding
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / 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 / N-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / Acharya, K.R. / Brew, K.
CitationJournal: Glycobiology / Year: 2008
Title: Screening a Limited Structure-Based Library Identifies Udp-Galnac-Specific Mutants of {Alpha}-1,3-Galactosyltransferase.
Authors: Tumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / Acharya, K.R. / Brew, K.
History
DepositionJul 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0203
Polymers32,5611
Non-polymers4592
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.197, 70.197, 126.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE / GALACTOSYLTRANSFERASE / UDP-GALACTOSE\: BETA-D-GALACTOSYL-1 / 4-N-ACETYL-D-GLUCOSAMINIDE ALPHA-1 / ...GALACTOSYLTRANSFERASE / UDP-GALACTOSE\: BETA-D-GALACTOSYL-1 / 4-N-ACETYL-D-GLUCOSAMINIDE ALPHA-1 / 3-GALACTOSYLTRANSFERASE / ALPHA-1 / 3 GALACTOSYLTRANSFERASE


Mass: 32560.500 Da / Num. of mol.: 1 / Fragment: RESIDUES 82-358 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: UDP-GALACTOSE / Source: (gene. exp.) BOS TAURUS (domestic cattle) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14769, N-acetyllactosaminide 3-alpha-galactosyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 280 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 281 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, HIS 280 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 281 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 282 TO GLY ENGINEERED RESIDUE IN CHAIN A, ILE 283 TO LEU

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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: 2.6 Å3/Da / Density % sol: 52.4 % / Description: NONE
Crystal growpH: 8
Details: PROTEIN: 5 MG/ML IN 20 MM MES-NAOH BUFFER, PH 6.0, 10% GLYCEROL, CONTAINING 10 MM MNCL2 AND 10 MM UDP-GALNAC MOTHER LIQUOR: 10-15% PEG 6000, 0.1 M TRIS-HCL, PH 8.0 AND 15-25% MPD

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 6, 2006 / Details: MIRROR
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 11624 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.04 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JCJ

2jcj


Resolution: 2.7→43.91 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 553 3 %RANDOM
Rwork0.192 ---
obs-18690 99.4 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.41 Å20 Å20 Å2
2---6.41 Å20 Å2
3---12.82 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 26 43 2369
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.405 -
Rwork0.264 650

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