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- PDB-4m4k: Crystal structure of the Drosphila beta,14galactosyltransferase 7... -

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Basic information

Entry
Database: PDB / ID: 4m4k
TitleCrystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose
ComponentsBeta-4-galactosyltransferase 7
KeywordsTRANSFERASE / GT-A glycosyltransferase family / UDP-Gal and 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 / GALACTOSE-URIDINE-5'-DIPHOSPHATE / : / Beta-1,4-galactosyltransferase 7
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Molecular Placement / Resolution: 2.2 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
DepositionAug 7, 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: Atomic model / Data collection ...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 / 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 / _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 2.2Nov 20, 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)34,2946
Polymers33,3191
Non-polymers9745
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.680, 82.680, 131.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 33319.305 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 71-311 / Mutation: D211N
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 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: 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, 177 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-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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

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 6000, 10% MPD, 1M NaCl, 10 mM MnCl2, 10 mM UDP-Gal and 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 28, 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: 2.2→50 Å / Num. all: 24123 / Num. obs: 23650 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 9.6 % / Rsym value: 0.077 / Net I/σ(I): 24.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2345 / Rsym value: 0.66 / % possible all: 99.7

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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 Placement
Starting model: PDB entry 4LW6

4lw6


Resolution: 2.2→36.976 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 987 5.12 %Random
Rwork0.1867 ---
obs0.188 23650 98 %-
all-24123 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→36.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 58 173 2213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072101
X-RAY DIFFRACTIONf_angle_d1.1372849
X-RAY DIFFRACTIONf_dihedral_angle_d12.846777
X-RAY DIFFRACTIONf_chiral_restr0.078309
X-RAY DIFFRACTIONf_plane_restr0.004361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27910.31911310.27792436X-RAY DIFFRACTION98
2.2791-2.38280.27411230.25182483X-RAY DIFFRACTION99
2.3828-2.50840.29181400.23382452X-RAY DIFFRACTION98
2.5084-2.66550.26331490.23662439X-RAY DIFFRACTION98
2.6655-2.87130.24831330.22922423X-RAY DIFFRACTION97
2.8713-3.16010.29261290.22632442X-RAY DIFFRACTION97
3.1601-3.6170.21851290.19232468X-RAY DIFFRACTION97
3.617-4.55570.16071500.15672546X-RAY DIFFRACTION99
4.5557-36.9760.18811260.16042751X-RAY DIFFRACTION100

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