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- PDB-5gw7: Crystal structure of the glycosynthase mutant E727A of Escherichi... -

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Basic information

Entry
Database: PDB / ID: 5gw7
TitleCrystal structure of the glycosynthase mutant E727A of Escherichia coli GH63 glycosidase in complex with glucose and lactose
ComponentsGlucosidase YgjK
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH63 ALPHA / ALPHA BARREL
Function / homology
Function and homology information


glucosidase complex / alpha,alpha-trehalase activity / trehalose catabolic process / glucosidase activity / oligosaccharide catabolic process / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / DNA damage response / metal ion binding
Similarity search - Function
Ribosomal protein L30p/L7e / : / Glucosidase YgjK, N-terminal / putative glycoside hydrolase family protein from bacillus halodurans / Helix Hairpins - #100 / Glycoside hydrolase, family 37 / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / Ribosomal Protein L30; Chain: A, / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 ...Ribosomal protein L30p/L7e / : / Glucosidase YgjK, N-terminal / putative glycoside hydrolase family protein from bacillus halodurans / Helix Hairpins - #100 / Glycoside hydrolase, family 37 / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / Ribosomal Protein L30; Chain: A, / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-lactose / beta-D-glucopyranose / Glucosidase YgjK
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMiyazaki, T. / Tonozuka, T.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting alpha-glycosidase
Authors: Miyazaki, T. / Nishikawa, A. / Tonozuka, T.
History
DepositionSep 8, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 12, 2016ID: 5CA4
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Category: chem_comp / citation / diffrn_source
Item: _chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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_conn_type / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 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: Glucosidase YgjK
B: Glucosidase YgjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,06710
Polymers171,8942
Non-polymers1,1748
Water12,394688
1
A: Glucosidase YgjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5345
Polymers85,9471
Non-polymers5874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27080 Å2
MethodPISA
2
B: Glucosidase YgjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5345
Polymers85,9471
Non-polymers5874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.740, 137.069, 81.599
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucosidase YgjK


Mass: 85946.781 Da / Num. of mol.: 2 / Mutation: E727A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ygjK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P42592, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 692 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 1.82 Å3/Da / Density % sol: 32.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 8000, 0.4 M magnesium chloride, 100 mM Tris-HCl buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 60457 / % possible obs: 97.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 6 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W7T

3w7t


Resolution: 2.2→47.09 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.217 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.526 / ESU R Free: 0.224 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20847 3005 5 %RANDOM
Rwork0.15423 ---
obs0.15693 57424 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20.03 Å2
2---0.03 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12127 0 74 688 12889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212589
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211504
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.93917128
X-RAY DIFFRACTIONr_angle_other_deg0.756326470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43451530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2524.322634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.776152011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6151575
X-RAY DIFFRACTIONr_chiral_restr0.0740.21795
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023072
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5473.1176093
X-RAY DIFFRACTIONr_mcbond_other1.5443.1166092
X-RAY DIFFRACTIONr_mcangle_it2.4024.677620
X-RAY DIFFRACTIONr_mcangle_other2.4024.6717621
X-RAY DIFFRACTIONr_scbond_it1.9383.3356496
X-RAY DIFFRACTIONr_scbond_other1.9383.3356497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1534.9049505
X-RAY DIFFRACTIONr_long_range_B_refined4.57525.37315780
X-RAY DIFFRACTIONr_long_range_B_other4.50325.29815601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 198 -
Rwork0.196 3829 -
obs--87.43 %

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