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- PDB-7cwi: Crystal structure of beta-galactosidase II from Bacillus circulans -

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Basic information

Entry
Database: PDB / ID: 7cwi
TitleCrystal structure of beta-galactosidase II from Bacillus circulans
Componentsbeta-galactosidase
KeywordsHYDROLASE / beta-galactosidase / CARBOHYDRATE
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
: / Beta-galactosidase-like, Galactose-binding 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 ...: / Beta-galactosidase-like, Galactose-binding 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 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 28, 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

Downloads & links

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Assembly

Deposited unit
A: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,11715
Polymers91,8611
Non-polymers1,25614
Water11,620645
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.802, 159.802, 96.167
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-1580-

HOH

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Components

#1: Protein beta-galactosidase


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 BL21(DE3) (bacteria) / References: UniProt: A0A6M5K904*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate, Sodium acetate/Acetic acid pH4, 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: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 101473 / % possible obs: 99.2 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Rrim(I) all: 0.088 / Χ2: 2.497 / Net I/σ(I): 12.3 / Num. measured all: 848695
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.985.60.29946820.8940.1260.3261.65592.4
1.98-2.026.40.28649650.930.1140.311.7498
2.02-2.066.80.27249900.9450.1060.2921.86698.5
2.06-2.170.24550360.9550.0940.2631.96399
2.1-2.157.20.22150250.970.0830.2372.09499.5
2.15-2.27.40.20350570.9760.0760.2172.1999.5
2.2-2.257.50.19250910.9780.0710.2062.26999.6
2.25-2.317.70.17650430.9830.0650.1882.28499.7
2.31-2.387.90.16550980.9870.060.1762.27199.7
2.38-2.468.10.15550680.9880.0560.1652.35799.7
2.46-2.548.30.14250820.9910.050.1512.42299.8
2.54-2.658.40.13150750.9910.0460.1392.50399.9
2.65-2.778.70.11750920.9940.040.1242.60399.8
2.77-2.9190.10551320.9950.0360.1112.77299.8
2.91-3.19.50.09250950.9950.0310.0982.91999.9
3.1-3.33100.0851430.9970.0260.0853.20799.8
3.33-3.6710.40.0751260.9970.0220.0743.3599.9
3.67-4.210.40.05951680.9980.0190.0623.08399.9
4.2-5.2910.40.05151830.9980.0160.0542.48799.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPJ

4ypj


Resolution: 1.95→31.77 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.428 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 5030 5 %RANDOM
Rwork0.1559 ---
obs0.1574 96434 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.85 Å2 / Biso mean: 25.912 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.37 Å20 Å2
2--0.75 Å2-0 Å2
3----2.43 Å2
Refinement stepCycle: final / Resolution: 1.95→31.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 73 645 7104
Biso mean--50.92 34.03 -
Num. residues----803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136648
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175853
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.6459030
X-RAY DIFFRACTIONr_angle_other_deg1.4831.5813598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7335810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96322.869366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.671536
X-RAY DIFFRACTIONr_chiral_restr0.0860.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021453
LS refinement shellResolution: 1.954→2.004 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 353 -
Rwork0.218 6692 -
all-7045 -
obs--93.73 %

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