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- PDB-3w7x: Crystal structure of E. coli YgjK D324N complexed with melibiose -

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Basic information

Entry
Database: PDB / ID: 3w7x
TitleCrystal structure of E. coli YgjK D324N complexed with melibiose
ComponentsUncharacterized protein YgjK
KeywordsHYDROLASE / GH63 / processing alpha-glucosidase I / alpha/alpha barrel
Function / homology
Function and homology information


glucosidase complex / alpha,alpha-trehalase activity / trehalose catabolic process / glucosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / oligosaccharide catabolic process / 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 / Trehalase / Glycoside hydrolase, family 37 / Helix Hairpins - #100 / : / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / Ribosomal Protein L30; Chain: A, ...Ribosomal protein L30p/L7e / : / Glucosidase YgjK, N-terminal / putative glycoside hydrolase family protein from bacillus halodurans / Trehalase / Glycoside hydrolase, family 37 / Helix Hairpins - #100 / : / 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-melibiose / Glucosidase YgjK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMiyazaki, T. / Ichikawa, M. / Yokoi, G. / Kitaoka, M. / Mori, H. / Kitano, Y. / Nishikawa, A. / Tonozuka, T.
CitationJournal: Febs J. / Year: 2013
Title: Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity.
Authors: Miyazaki, T. / Ichikawa, M. / Yokoi, G. / Kitaoka, M. / Mori, H. / Kitano, Y. / Nishikawa, A. / Tonozuka, T.
History
DepositionMar 8, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _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_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym.entity_id / _struct_ref_seq_dif.details
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 6, 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: Uncharacterized protein YgjK
B: Uncharacterized protein YgjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,7726
Polymers172,0082
Non-polymers7654
Water2,702150
1
A: Uncharacterized protein YgjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3863
Polymers86,0041
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein YgjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3863
Polymers86,0041
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.140, 138.160, 86.200
Angle α, β, γ (deg.)90.00, 98.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein YgjK


Mass: 86003.836 Da / Num. of mol.: 2 / Mutation: D324N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3080, JW3051, ygjK / Plasmid: pYgjK-SIG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P42592
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose / alpha-melibiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-melibiose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 8000, 0.6M magnesium chloride, 100mM Tris-HCl buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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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 210r / Detector: CCD / Date: Nov 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 38773 / % possible obs: 98 % / Rmerge(I) obs: 0.116
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.9 / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C68

3c68
PDB Unreleased entry


Resolution: 2.7→40.52 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24899 1796 5 %RANDOM
Rwork0.18861 ---
obs0.19173 34084 90.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.066 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12154 0 48 150 12352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212545
X-RAY DIFFRACTIONr_bond_other_d00.0211467
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.93717059
X-RAY DIFFRACTIONr_angle_other_deg3.652326372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17651520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46424.416634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.666152007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3641572
X-RAY DIFFRACTIONr_chiral_restr0.0640.21781
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02114472
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023060
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_it0.341.57562
X-RAY DIFFRACTIONr_mcbond_other0.0461.53082
X-RAY DIFFRACTIONr_mcangle_it0.654212145
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.88134981
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5234.54910
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 104 -
Rwork0.234 2031 -
obs--75.02 %

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