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- PDB-4lw6: Crystal structure of catalytic domain of Drosophila beta1,4galact... -

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Basic information

Entry
Database: PDB / ID: 4lw6
TitleCrystal structure of catalytic domain of Drosophila beta1,4galactosyltransferase 7 complex with xylobiose
ComponentsBeta-4-galactosyltransferase 7
KeywordsTRANSFERASE / GT-A glycosyltransferase family / Xylose / 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
4beta-beta-xylobiose / : / 2-AMINO-1,3-PROPANEDIOL / URIDINE-5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 7
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsQasba, P.K. / Ramakrishnan, B.
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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1535
Polymers33,3201
Non-polymers8324
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.943, 81.943, 133.053
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-600-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 33320.293 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 71-311
Source method: isolated from a genetically manipulated source
Details: expressed as inclusion bodies and in vitro refolded
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: 4galactosyltransferase, 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: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 105 molecules

#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: Chemical ChemComp-SEL / 2-AMINO-1,3-PROPANEDIOL / SERINOL


Type: L-peptide linking / Mass: 91.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM HEPES, 5% PEG 6000, 10% MPD, 100 mM Serinol, 10 mM xylobiose, 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: 2.4→50 Å / Num. obs: 17496 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rsym value: 0.074 / Net I/σ(I): 21.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1392 / Rsym value: 0.65 / % possible all: 77

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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: 2.4→39.004 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 889 5.13 %Random
Rwork0.177 ---
obs0.1789 17342 94.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→39.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 51 102 2135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142095
X-RAY DIFFRACTIONf_angle_d1.5572837
X-RAY DIFFRACTIONf_dihedral_angle_d15.746781
X-RAY DIFFRACTIONf_chiral_restr0.092304
X-RAY DIFFRACTIONf_plane_restr0.006361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.32471500.27832268X-RAY DIFFRACTION81
2.55-2.74680.2961570.25322681X-RAY DIFFRACTION95
2.7468-3.02320.31530.23472764X-RAY DIFFRACTION97
3.0232-3.46040.26361480.19952837X-RAY DIFFRACTION98
3.4604-4.35880.171430.15152894X-RAY DIFFRACTION98
4.3588-39.0040.16791380.14793009X-RAY DIFFRACTION97

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