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- PDB-5yif: Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, E163A ... -

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Basic information

Entry
Database: PDB / ID: 5yif
TitlePyruvylated beta-D-galactosidase from Bacillus sp. HMA207, E163A mutant pyruvylated beta-D-galactose complex
ComponentsPyruvylated beta-D-galactosidase
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-8VR / Glycoside hydrolase family 1 protein
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTanuma, M. / Yamada, C. / Arakawa, T. / Higuchi, Y. / Takegawa, K. / Fushinobu, S.
CitationJournal: Sci Rep / Year: 2018
Title: Identification and characterization of a novel beta-D-galactosidase that releases pyruvylated galactose.
Authors: Higuchi, Y. / Matsufuji, H. / Tanuma, M. / Arakawa, T. / Mori, K. / Yamada, C. / Shofia, R. / Matsunaga, E. / Tashiro, K. / Fushinobu, S. / Takegawa, K.
History
DepositionOct 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvylated beta-D-galactosidase
B: Pyruvylated beta-D-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4894
Polymers110,9892
Non-polymers5002
Water3,009167
1
A: Pyruvylated beta-D-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7452
Polymers55,4941
Non-polymers2501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyruvylated beta-D-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7452
Polymers55,4941
Non-polymers2501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.780, 114.780, 150.434
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21B-601-

HOH

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Components

#1: Protein Pyruvylated beta-D-galactosidase


Mass: 55494.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: HMA207 / Gene: ORF1119 / Plasmid: pET32b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): codon plus RIL / References: UniProt: A0A2B9BPQ7*PLUS
#2: Chemical ChemComp-8VR / (2R,4aR,6R,7R,8R,8aR)-2-methyl-6,7,8-tris(oxidanyl)-4,4a,6,7,8,8a-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic acid


Mass: 250.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 32% PEG 300, 0.1 M phosphate-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2017
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→100 Å / Num. obs: 42682 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 45.897 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.1
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2129 / CC1/2: 0.621 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YHS

5yhs


Resolution: 2.45→99.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.102 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.295 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27001 2049 4.8 %RANDOM
Rwork0.20627 ---
obs0.20925 40594 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.497 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: 1 / Resolution: 2.45→99.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7576 0 34 167 7777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.027844
X-RAY DIFFRACTIONr_bond_other_d0.0060.027192
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.93810632
X-RAY DIFFRACTIONr_angle_other_deg1.1163.00216578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3875914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55524.25400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.718151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9691530
X-RAY DIFFRACTIONr_chiral_restr0.1120.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028840
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021918
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_it2.8564.2933668
X-RAY DIFFRACTIONr_mcbond_other2.8544.2923667
X-RAY DIFFRACTIONr_mcangle_it4.3646.4254578
X-RAY DIFFRACTIONr_mcangle_other4.3656.4274579
X-RAY DIFFRACTIONr_scbond_it3.1534.5584176
X-RAY DIFFRACTIONr_scbond_other3.1534.5584176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8866.7156055
X-RAY DIFFRACTIONr_long_range_B_refined6.71449.329197
X-RAY DIFFRACTIONr_long_range_B_other6.71549.2849180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.449→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 143 -
Rwork0.28 2947 -
obs--99.55 %

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