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- PDB-5gsl: Glycoside hydrolase A -

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Basic information

Entry
Database: PDB / ID: 5gsl
TitleGlycoside hydrolase A
Components778aa long hypothetical beta-galactosidase
KeywordsHYDROLASE / Glycoside hydrolase TIM-barrel
Function / homology
Function and homology information


2-acetamido-4-O-(2-amino-2-deoxy-beta-D-glucopyranosyl)-2-deoxy-D-glucose exo-beta-D-glucosaminidase activity / beta-galactosidase complex / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / beta-galactosidase activity / chitin catabolic process / carbohydrate metabolic process / cytoplasm
Similarity search - Function
: / GLMA-like, C-terminal / GLMA-like, glycosyl hydrolase domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Exo-beta-D-glucosaminidase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsWatanabe, M. / Kamachi, S. / Mine, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
The Japan Society for the Promotion of Sciences25450143 Japan
CitationJournal: To Be Published
Title: Glycoside hydrolase A
Authors: Watanabe, M. / Kamachi, S. / Mine, S.
History
DepositionAug 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 778aa long hypothetical beta-galactosidase
B: 778aa long hypothetical beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,8515
Polymers182,5662
Non-polymers2853
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-31 kcal/mol
Surface area49430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.843, 148.767, 165.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein 778aa long hypothetical beta-galactosidase / Glycoside hydrolase A


Mass: 91283.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0511 / Production host: Escherichia coli (E. coli) / References: UniProt: O58247
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris-HCl pH8.5, 20% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 51643 / % possible obs: 92.2 % / Redundancy: 4 % / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.849 / SU B: 18.839 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.403 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28778 2568 5 %RANDOM
Rwork0.21721 ---
obs0.22076 49025 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.318 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2---0.77 Å20 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12884 0 15 134 13033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913260
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212478
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.95717990
X-RAY DIFFRACTIONr_angle_other_deg1.006328676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03851548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18523.214672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.257152264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.66415102
X-RAY DIFFRACTIONr_chiral_restr0.0930.21880
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114818
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023212
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_it2.0724.0366198
X-RAY DIFFRACTIONr_mcbond_other2.0724.0356197
X-RAY DIFFRACTIONr_mcangle_it3.5046.0517744
X-RAY DIFFRACTIONr_mcangle_other3.5046.0527745
X-RAY DIFFRACTIONr_scbond_it1.9744.2127062
X-RAY DIFFRACTIONr_scbond_other1.9654.2077050
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4156.21210228
X-RAY DIFFRACTIONr_long_range_B_refined5.88631.54115032
X-RAY DIFFRACTIONr_long_range_B_other5.88531.54815027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 175 -
Rwork0.377 3210 -
obs--82.7 %

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