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- PDB-7cwd: Crystal structure of beta-galactosidase II from Bacillus circulan... -

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Basic information

Entry
Database: PDB / ID: 7cwd
TitleCrystal structure of beta-galactosidase II from Bacillus circulans in complex with beta-D-galactopyranosyl disaccharide
Componentsbeta-glalactosidase
KeywordsHYDROLASE / beta-galactosidase / CARBOHYDRATE
Function / homology
Function and homology information


beta-galactosidase / carbohydrate catabolic process / beta-galactosidase activity
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 / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
beta-D-galactopyranose / alpha-D-glucopyranose / beta-galactosidase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHong, H. / Seo, H.
CitationJournal: J.Agric.Food Chem. / Year: 2020
Title: High Galacto-Oligosaccharide Production and a Structural Model for Transgalactosylation of beta-Galactosidase II from Bacillus circulans .
Authors: Choi, J.Y. / Hong, H. / Seo, H. / Pan, J.G. / Kim, E.J. / Maeng, P.J. / Yang, T.H. / Kim, K.J.
History
DepositionAug 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: beta-glalactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4014
Polymers91,8611
Non-polymers5403
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint7 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.499, 159.499, 96.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1122-

HOH

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Components

#1: Protein beta-glalactosidase


Mass: 91860.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6M5K904*PLUS, beta-galactosidase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsGLC A 901 and GAL A 903 existed in alternate conformations in this structure.
Sequence detailsTHE SEQUENCE HAS BEEN DEPOSITED TO GENBANK WITH ACCESSION NUMBER QJU69416.

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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: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Ammonium sulfate, Sodium acetate, Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 89811 / % possible obs: 94.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Χ2: 2.066 / Net I/σ(I): 11.4 / Num. measured all: 497629
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.80.29746200.940.1460.3331.41299.4
2.03-2.075.10.29346740.9390.1380.3251.60299.4
2.07-2.115.30.26846770.9510.1250.2961.60799.6
2.11-2.155.30.23446870.9740.1090.2591.65699.4
2.15-2.24.60.20745540.9740.10.2311.68897.2
2.2-2.252.20.17324960.9090.1170.2112.46353.2
2.25-2.313.20.16835010.9750.0910.1921.99574
2.31-2.375.30.17146630.9840.0780.1891.73399.1
2.37-2.445.60.16147070.9860.0720.1771.80799.4
2.44-2.525.70.14646970.990.0650.1611.80899.5
2.52-2.615.80.13246680.990.0580.1451.8499.3
2.61-2.715.90.11946860.9920.0520.131.91699.6
2.71-2.846.20.10747130.9920.0450.1171.96299.3
2.84-2.996.50.09346920.9940.0390.1012.08899.5
2.99-3.176.60.0847050.9960.0330.0862.20999.1
3.17-3.426.40.0746960.9960.0290.0762.50798.9
3.42-3.765.10.07344470.9860.0360.0823.40993.6
3.76-4.3150.05244210.9970.0240.0572.54592
4.31-5.437.10.05247200.9970.0210.0562.36198.1
5.43-506.80.05447870.9970.0220.0582.62496.4

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Processing

Software
NameVersionClassification
REFMACv5.0refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data collection
MOLREPphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPJ

4ypj


Resolution: 2→33.28 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4778 -RANDOM
Rwork0.189 ---
obs-89811 99.4 %-
Displacement parametersBiso max: 106.34 Å2 / Biso mean: 29.9466 Å2 / Biso min: 8.91 Å2
Refinement stepCycle: LAST / Resolution: 2→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 35 335 6756
LS refinement shellResolution: 2→2.03 Å

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