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- PDB-6qud: 2-deoxy-galactose reaction intermediate of a Truncated beta-galac... -

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Basic information

Entry
Database: PDB / ID: 6qud
Title2-deoxy-galactose reaction intermediate of a Truncated beta-galactosidase III from Bifidobacterium bifidum
ComponentsBeta-galactosidase
KeywordsSUGAR BINDING PROTEIN / TIM BARREL / GLYCOSIDE HYDROLASE / HYDROLASE
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain ...Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-deoxy-alpha-D-galactopyranose / Beta-galactosidase
Similarity search - Component
Biological speciesBifidobacterium bifidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsThirup, S.S. / Nielsen, J.A. / Andersen, J.L. / Alsarraf, H. / Blaise, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Agency for Science Technology and Innovation Denmark
CitationJournal: To Be Published
Title: Truncated beta-galactosidase III from Bifidobacterium bifidum
Authors: Nielsen, J.A. / Andersen, J.L. / Alsarraf, H. / Blaise, M. / Thirup, S.S. / Larsen, M.K. / Cramer, J.F.
History
DepositionFeb 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5633
Polymers95,3591
Non-polymers2042
Water13,529751
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-8 kcal/mol
Surface area31280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.210, 53.920, 112.620
Angle α, β, γ (deg.)90.00, 106.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-galactosidase


Mass: 95358.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q9F4D5, beta-galactosidase
#2: Sugar ChemComp-2DG / 2-deoxy-alpha-D-galactopyranose / 2-deoxy-alpha-D-lyxo-hexopyranose / 2-deoxy-alpha-D-galactose / 2-deoxy-D-galactose / 2-deoxy-galactose


Type: D-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 23 % PEG 1500 5 mM glucose 10 mM Tris:HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 2.1→42 Å / Num. obs: 46763 / % possible obs: 98 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2 / Num. unique obs: 4583 / CC1/2: 0.756 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QUC

6quc


Resolution: 2.1→41.811 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9
RfactorNum. reflection% reflection
Rfree0.2086 1588 3.4 %
Rwork0.1653 --
obs0.1668 46762 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6371 0 11 751 7133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026530
X-RAY DIFFRACTIONf_angle_d0.578891
X-RAY DIFFRACTIONf_dihedral_angle_d11.8063793
X-RAY DIFFRACTIONf_chiral_restr0.045986
X-RAY DIFFRACTIONf_plane_restr0.0031151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.26941370.23444027X-RAY DIFFRACTION97
2.1678-2.24520.30011410.26064078X-RAY DIFFRACTION99
2.2452-2.33510.29011460.24084108X-RAY DIFFRACTION99
2.3351-2.44140.27991450.20464084X-RAY DIFFRACTION99
2.4414-2.57010.27211470.19634078X-RAY DIFFRACTION98
2.5701-2.73110.24671360.18764031X-RAY DIFFRACTION97
2.7311-2.94190.22181470.17764147X-RAY DIFFRACTION99
2.9419-3.23790.22461470.16724130X-RAY DIFFRACTION99
3.2379-3.70620.20661440.14814112X-RAY DIFFRACTION98
3.7062-4.66840.14941480.1234134X-RAY DIFFRACTION98
4.6684-41.81890.13881500.12364245X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.85290.610.80320.8106-0.30442.65330.062-0.08220.02830.0873-0.00370.10360.087-0.1731-0.06930.203-0.01330.02040.11540.00930.2183-11.4453-11.8869-27.591
21.02330.16380.67840.3677-0.13151.1808-0.10940.01340.117-0.06950.02850.0635-0.1432-0.0130.07750.20190.0153-0.00170.1272-0.02020.2203-4.4210.3345-40.6037
31.19570.54760.30281.05590.21781.1409-0.05920.12-0.1326-0.11090.0642-0.07160.10110.27440.01870.19090.0370.02080.19360.01430.21268.0802-1.3652-39.1914
40.52670.06890.1460.51670.00451.3942-0.00170.0057-0.03960.0339-0.0203-0.0936-0.04410.49070.0140.1731-0.0214-0.0030.39330.01480.239927.39656.7968-18.7855
51.59750.13820.36821.11590.32291.3766-0.0163-0.22690.07580.0805-0.03130.0333-0.129-0.00970.02090.20590.0070.01810.2385-0.01190.16986.66126.0143-4.7775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 370 )
3X-RAY DIFFRACTION3chain 'A' and (resid 371 through 535 )
4X-RAY DIFFRACTION4chain 'A' and (resid 536 through 776 )
5X-RAY DIFFRACTION5chain 'A' and (resid 777 through 912 )

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