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- PDB-5yhs: Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, apo form -

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Basic information

Entry
Database: PDB / ID: 5yhs
TitlePyruvylated beta-D-galactosidase from Bacillus sp. HMA207, apo form
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
Glycoside hydrolase family 1 protein
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionSep 29, 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


Theoretical massNumber of molelcules
Total (without water)111,1052
Polymers111,1052
Non-polymers00
Water1,44180
1
A: Pyruvylated beta-D-galactosidase


Theoretical massNumber of molelcules
Total (without water)55,5521
Polymers55,5521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyruvylated beta-D-galactosidase


Theoretical massNumber of molelcules
Total (without water)55,5521
Polymers55,5521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.997, 113.997, 148.678
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Pyruvylated beta-D-galactosidase


Mass: 55552.406 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: Hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 50% PEG300, 0.1M phosphate-citrate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 14, 2016
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 39354 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 56.122 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1925 / CC1/2: 0.777 / % possible all: 100

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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: 3TA9

3ta9


Resolution: 2.5→98.72 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 13.716 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.314 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27625 2053 5.2 %RANDOM
Rwork0.21936 ---
obs0.22237 37262 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.492 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: 0.292 Å
Refinement stepCycle: 1 / Resolution: 2.5→98.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7382 0 0 80 7462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197606
X-RAY DIFFRACTIONr_bond_other_d0.0060.026968
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.93110298
X-RAY DIFFRACTIONr_angle_other_deg1.085316050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6965886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43324.271398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.039151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1291530
X-RAY DIFFRACTIONr_chiral_restr0.1050.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028610
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021880
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_it3.7835.5043562
X-RAY DIFFRACTIONr_mcbond_other3.7815.5023561
X-RAY DIFFRACTIONr_mcangle_it5.6148.2354442
X-RAY DIFFRACTIONr_mcangle_other5.6148.2364443
X-RAY DIFFRACTIONr_scbond_it3.6265.7714044
X-RAY DIFFRACTIONr_scbond_other3.6265.7724045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6198.5295857
X-RAY DIFFRACTIONr_long_range_B_refined7.74262.6518889
X-RAY DIFFRACTIONr_long_range_B_other7.74262.6598887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 116 -
Rwork0.333 2709 -
obs--99.58 %

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