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- PDB-5gsm: Glycoside hydrolase B with product -

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Basic information

Entry
Database: PDB / ID: 5gsm
TitleGlycoside hydrolase B with product
ComponentsExo-beta-D-glucosaminidaseExo-1,4-beta-D-glucosaminidase
KeywordsHYDROLASE / Glycoside hydrolase TIM-barrel
Function / homology
Function and homology information


beta-galactosidase complex / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / vacuole / chitin catabolic process / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
2-amino-2-deoxy-beta-D-glucopyranose / DI(HYDROXYETHYL)ETHER / PROPANOIC ACID / Exo-beta-D-glucosaminidase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.27 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 B with product
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: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exo-beta-D-glucosaminidase
B: Exo-beta-D-glucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,25226
Polymers180,6712
Non-polymers2,58124
Water23,0951282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint71 kcal/mol
Surface area50540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.585, 119.991, 85.902
Angle α, β, γ (deg.)90.00, 98.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Exo-beta-D-glucosaminidase / Exo-1,4-beta-D-glucosaminidase / Glycoside hydrolase B


Mass: 90335.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: Tk-Glm, TK1754 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS / References: UniProt: Q76HN4
#2: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE / Glucosamine


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1304 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H6O2
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1282 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM PCB buffer pH7.0, 25% (w/v) PEG 1500, 50mM GlcN

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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: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 370867 / % possible obs: 92.5 % / Redundancy: 2.9 % / Net I/σ(I): 20.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.27→20 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.003 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17543 18716 5 %RANDOM
Rwork0.13026 ---
obs0.13251 352051 92.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.56 Å2
2--0.69 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.27→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12794 0 172 1282 14248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.01913454
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212634
X-RAY DIFFRACTIONr_angle_refined_deg2.4441.96918262
X-RAY DIFFRACTIONr_angle_other_deg1.2163.00129115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91251600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09723.189646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.248152179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8731595
X-RAY DIFFRACTIONr_chiral_restr0.1690.21912
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02114998
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023171
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_it2.0441.086331
X-RAY DIFFRACTIONr_mcbond_other2.0341.086330
X-RAY DIFFRACTIONr_mcangle_it2.4771.6347924
X-RAY DIFFRACTIONr_mcangle_other2.4821.6347925
X-RAY DIFFRACTIONr_scbond_it4.6911.4977123
X-RAY DIFFRACTIONr_scbond_other4.6911.4977123
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2852.09210329
X-RAY DIFFRACTIONr_long_range_B_refined4.90610.62716517
X-RAY DIFFRACTIONr_long_range_B_other4.90610.6316518
X-RAY DIFFRACTIONr_rigid_bond_restr5.267326088
X-RAY DIFFRACTIONr_sphericity_free30.9475329
X-RAY DIFFRACTIONr_sphericity_bonded12.735526662
LS refinement shellResolution: 1.271→1.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 1221 -
Rwork0.289 22791 -
obs--81.23 %

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