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- PDB-4lw3: Crystal structure of the Drosophila beta1,4galactosyltransferase7... -

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Basic information

Entry
Database: PDB / ID: 4lw3
TitleCrystal structure of the Drosophila beta1,4galactosyltransferase7 catalytic domain D211N single mutant enzyme complex with manganese and UDP-galactose
ComponentsBeta-4-galactosyltransferase 7
KeywordsTRANSFERASE / GT-A glycosyltransferase family / manganese and UDp-galactose / Golgi
Function / homology
Function and homology information


glycosaminoglycan-protein linkage region biosynthetic process / xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / Glycosaminoglycan-protein linkage region biosynthesis / : / proteoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / N-glycan processing / carbohydrate metabolic process ...glycosaminoglycan-protein linkage region biosynthetic process / xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / Glycosaminoglycan-protein linkage region biosynthesis / : / proteoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / N-glycan processing / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / metal ion binding
Similarity search - Function
Beta-1,4-galactosyltransferase / Galactosyltransferase, N-terminal / N-terminal region of glycosyl transferase group 7 / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / 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
GALACTOSE-URIDINE-5'-DIPHOSPHATE / : / Beta-1,4-galactosyltransferase 7
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRamakrishnan, B. / Qasba, P.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structures of beta-1,4-Galactosyltransferase 7 Enzyme Reveal Conformational Changes and Substrate Binding.
Authors: Tsutsui, Y. / Ramakrishnan, B. / Qasba, P.K.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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: Beta-4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9413
Polymers33,3191
Non-polymers6212
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.087, 82.087, 133.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

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Components

#1: Protein Beta-4-galactosyltransferase 7 / FI08434p


Mass: 33319.305 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 71-311 / Mutation: D221N
Source method: isolated from a genetically manipulated source
Details: Protein expressed as inclusion bodies and in vitro refolded
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: 4-galactosyltransferase-7, beta-4GalT7, beta1, beta4GalT7, beta4GalT7-RA, CG11780, Dmel_CG11780
Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9VBZ9, Transferases; Glycosyltransferases; Hexosyltransferases, xylosylprotein 4-beta-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-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM HEPES, 5% PEG 6K, 10% MPD, 2 mM MnCl2, 2 mM UDP-Gal, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 17, 2013 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29731 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Rsym value: 0.057 / Net I/σ(I): 36.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2614 / Rsym value: 0.353 / % possible all: 85.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LW6

3lw6


Resolution: 2→28.913 Å / SU ML: 0.2 / Cross valid method: Throught / σ(F): 1.33 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 1536 5.05 %random
Rwork0.174 ---
obs0.1757 26249 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 37 304 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072128
X-RAY DIFFRACTIONf_angle_d1.1052886
X-RAY DIFFRACTIONf_dihedral_angle_d13.417801
X-RAY DIFFRACTIONf_chiral_restr0.076308
X-RAY DIFFRACTIONf_plane_restr0.004370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06420.27341090.21742252X-RAY DIFFRACTION84
2.0642-2.1380.24021230.20032559X-RAY DIFFRACTION96
2.138-2.22360.25541240.19792613X-RAY DIFFRACTION97
2.2236-2.32470.26481480.19182595X-RAY DIFFRACTION98
2.3247-2.44720.26281340.19172637X-RAY DIFFRACTION98
2.4472-2.60040.24841530.20012607X-RAY DIFFRACTION97
2.6004-2.80110.21741480.19852631X-RAY DIFFRACTION97
2.8011-3.08270.24881230.22656X-RAY DIFFRACTION97
3.0827-3.52810.20681490.17082663X-RAY DIFFRACTION97
3.5281-4.44240.18481620.14122732X-RAY DIFFRACTION99
4.4424-28.9130.16521630.16462913X-RAY DIFFRACTION99

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