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- PDB-8h25: Lacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230 -

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Basic information

Entry
Database: PDB / ID: 8h25
TitleLacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230
ComponentsBeta-galactosidase
KeywordsHYDROLASE / beta-galactosidase / GH35 / lacto-N-biose 1 / galacto-N-biose
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Beta-galactosidase 1-like / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel ...Beta-galactosidase 1-like / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-galactosidase
Similarity search - Component
Biological speciesLacticaseibacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsSaburi, W. / Ota, T. / Kato, K. / Tagami, T. / Yamashita, K. / Yao, M. / Mori, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Appl Glycosci (1999) / Year: 2023
Title: Function and Structure of Lacticaseibacillus casei GH35 beta-Galactosidase LBCZ_0230 with High Hydrolytic Activity to Lacto- N -biose I and Galacto- N -biose.
Authors: Saburi, W. / Ota, T. / Kato, K. / Tagami, T. / Yamashita, K. / Yao, M. / Mori, H.
History
DepositionOct 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,07915
Polymers275,3974
Non-polymers1,68211
Water6,630368
1
A: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,81210
Polymers137,6982
Non-polymers1,1138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint20 kcal/mol
Surface area39770 Å2
MethodPISA
2
B: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2675
Polymers137,6982
Non-polymers5693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint8 kcal/mol
Surface area39210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.384, 110.998, 120.337
Angle α, β, γ (deg.)90.000, 90.015, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 593 / Label seq-ID: 2 - 593

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Beta-galactosidase


Mass: 68849.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lacticaseibacillus casei (bacteria) / Gene: FEI12_08385 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5R8LFD3
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES-NaOH buffer (pH 7.5), 10% (v/v) 2-propanol, and 200 g/L polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5121
pseudo-merohedral22-h,-k,l20.4879
ReflectionResolution: 2.29→45.9 Å / Num. obs: 108220 / % possible obs: 99.7 % / Redundancy: 3.79 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.24
Reflection shellResolution: 2.29→2.43 Å / Mean I/σ(I) obs: 2.38 / Num. unique obs: 17244 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E8D

4e8d


Resolution: 2.295→45.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.982 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.232 5374 4.966 %
Rwork0.1947 102845 -
all0.197 --
obs-108219 99.618 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.496 Å2
Baniso -1Baniso -2Baniso -3
1-33.108 Å20 Å2-16.524 Å2
2---10.218 Å2-0 Å2
3----22.891 Å2
Refinement stepCycle: LAST / Resolution: 2.295→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19016 0 108 368 19492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01219710
X-RAY DIFFRACTIONr_bond_other_d0.0010.01617256
X-RAY DIFFRACTIONr_angle_refined_deg0.8861.65426825
X-RAY DIFFRACTIONr_angle_other_deg0.3171.56540259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58452366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.791588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.583103033
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.503101001
X-RAY DIFFRACTIONr_chiral_restr0.0450.22794
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024078
X-RAY DIFFRACTIONr_nbd_refined0.1950.23703
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.216331
X-RAY DIFFRACTIONr_nbtor_refined0.1790.29298
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.210002
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2576
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0370.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.235
X-RAY DIFFRACTIONr_nbd_other0.2230.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.23
X-RAY DIFFRACTIONr_mcbond_it2.2194.489473
X-RAY DIFFRACTIONr_mcbond_other2.2194.489473
X-RAY DIFFRACTIONr_mcangle_it3.3196.71611836
X-RAY DIFFRACTIONr_mcangle_other3.3196.71711837
X-RAY DIFFRACTIONr_scbond_it2.0774.62410237
X-RAY DIFFRACTIONr_scbond_other2.0764.62310235
X-RAY DIFFRACTIONr_scangle_it3.1796.87514989
X-RAY DIFFRACTIONr_scangle_other3.1796.87514990
X-RAY DIFFRACTIONr_lrange_it4.95254.37521437
X-RAY DIFFRACTIONr_lrange_other4.94454.30321411
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.0520169
X-RAY DIFFRACTIONr_ncsr_local_group_20.0510.0520602
X-RAY DIFFRACTIONr_ncsr_local_group_30.0790.0520220
X-RAY DIFFRACTIONr_ncsr_local_group_40.0780.0520169
X-RAY DIFFRACTIONr_ncsr_local_group_50.0510.0520633
X-RAY DIFFRACTIONr_ncsr_local_group_60.0790.0520175
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.081470.05011
12AX-RAY DIFFRACTIONLocal ncs0.081470.05011
23AX-RAY DIFFRACTIONLocal ncs0.05140.05011
24AX-RAY DIFFRACTIONLocal ncs0.05140.05011
35AX-RAY DIFFRACTIONLocal ncs0.078740.05011
36AX-RAY DIFFRACTIONLocal ncs0.078740.05011
47AX-RAY DIFFRACTIONLocal ncs0.078160.05011
48AX-RAY DIFFRACTIONLocal ncs0.078160.05011
59AX-RAY DIFFRACTIONLocal ncs0.051090.05011
510AX-RAY DIFFRACTIONLocal ncs0.051090.05011
611AX-RAY DIFFRACTIONLocal ncs0.079190.05011
612AX-RAY DIFFRACTIONLocal ncs0.079190.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.295-2.3540.5183700.4057360X-RAY DIFFRACTION96.7944
2.354-2.4190.4054070.3677422X-RAY DIFFRACTION99.9745
2.419-2.4890.373720.3217206X-RAY DIFFRACTION99.9736
2.489-2.5650.3293680.2916979X-RAY DIFFRACTION100
2.565-2.6490.3213630.2456793X-RAY DIFFRACTION99.9162
2.649-2.7420.3133490.2426539X-RAY DIFFRACTION100
2.742-2.8460.2893290.2296350X-RAY DIFFRACTION99.9102
2.846-2.9620.2683080.2186073X-RAY DIFFRACTION99.9217
2.962-3.0930.2813140.2085900X-RAY DIFFRACTION99.9517
3.093-3.2440.2172870.1795581X-RAY DIFFRACTION99.8809
3.244-3.420.2082810.1815344X-RAY DIFFRACTION99.9289
3.42-3.6270.1952700.185017X-RAY DIFFRACTION99.8678
3.627-3.8770.1842600.1724731X-RAY DIFFRACTION99.581
3.877-4.1870.1912130.1554426X-RAY DIFFRACTION99.7849
4.187-4.5870.1411950.1354093X-RAY DIFFRACTION99.7441
4.587-5.1270.1782020.1373666X-RAY DIFFRACTION99.6907
5.127-5.9180.1791730.1473232X-RAY DIFFRACTION99.7364
5.918-7.2440.1811360.1592798X-RAY DIFFRACTION99.762

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