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- PDB-2jck: Crystal structure of alpha-1,3 Galactosyltransferase (R365K) in c... -

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Basic information

Entry
Database: PDB / ID: 2jck
TitleCrystal structure of alpha-1,3 Galactosyltransferase (R365K) in complex with UDP and 2 manganese ion
ComponentsN-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE / SUBSTRATE SPECIFICITY / 3 GALACTOSYLTRANSFERASE / ALPHA-1 / ENZYME MECHANISM / GLYCOSYLTRANSFERASE GALACTOSYLTRANSFERASE / TRANSMEMBRANE / GOLGI APPARATUS / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / MEMBRANE / MANGANESE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / lipid glycosylation / Golgi cisterna membrane / glycosyltransferase activity / protein glycosylation / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJamaluddin, H. / Tumbale, P. / Withers, S.G. / Acharya, K.R. / Brew, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Conformational Changes Induced by Binding Udp-2F-Galactose to Alpha-1,3 Galactosyltransferase-Implications for Catalysis.
Authors: Jamaluddin, H. / Tumbale, P. / Withers, S.G. / Acharya, K.R. / Brew, K.
History
DepositionDec 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,5764
Polymers34,0621
Non-polymers5143
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)122.824, 68.251, 44.732
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2200-

HOH

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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


Mass: 34062.148 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 80-368 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: URIDINE-5'-DIPHOSPHATE (UDP), MANGANESE ION / Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14769, EC: 2.4.1.151, N-acetyllactosaminide 3-alpha-galactosyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 365 TO LYS

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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: 2.76 Å3/Da / Density % sol: 55 %
Crystal growpH: 8 / Details: 0.1M TRIS-HCL, PH 8.0, 10% PEG 6000, AND 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 25, 2005 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 34457 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.14 / % possible all: 93.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4V

1k4v


Resolution: 1.8→24.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 188273.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1015 3.3 %RANDOM
Rwork0.182 ---
obs0.182 31104 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2271 Å2 / ksol: 0.383987 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å2-3.03 Å2
2---2.83 Å20 Å2
3---4.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 27 409 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.651.5
X-RAY DIFFRACTIONc_mcangle_it1.062
X-RAY DIFFRACTIONc_scbond_it1.092
X-RAY DIFFRACTIONc_scangle_it1.652.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.213 168 3.3 %
Rwork0.214 4994 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMUDP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4UDP.PAR

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