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- PDB-6etz: Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB -

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Basic information

Entry
Database: PDB / ID: 6etz
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB
ComponentsBeta-galactosidase
KeywordsHYDROLASE / galactosidase / cold-adapted / psychrophilic / dimeric
Function / homology
Function and homology information


lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding
Similarity search - Function
Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 ...Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / 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
ACETATE ION / MALONATE ION / beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRutkiewicz-Krotewicz, M. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2016/21/B/ST5/00555 Poland
Citation
Journal: Crystals / Year: 2018
Title: In Situ Random Microseeding and Streak Seeding Used for Growth of Crystals of Cold-Adapted Beta-D-Galactosidases: Crystal Structure of BetaDG from Arthrobacter sp. 32cB
Authors: Rutkiewicz-Krotewicz, M. / Pietrzyk-Brzezinska, A.J. / Wanarska, M. / Cieslinski, H. / Bujacz, A.
#1: Journal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Structural features of cold-adapted dimeric GH2 beta-D-galactosidase from Arthrobacter sp. 32cB.
Authors: Rutkiewicz, M. / Bujacz, A. / Bujacz, G.
History
DepositionOct 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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)108,1307
Polymers107,7681
Non-polymers3616
Water21,2941182
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,25914
Polymers215,5372
Non-polymers72212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5900 Å2
ΔGint-33 kcal/mol
Surface area68320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.784, 137.784, 127.208
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Beta-galactosidase


Mass: 107768.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. 32cB (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023UGN9, beta-galactosidase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1182 / 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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 35% Tacsimate pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→46.73 Å / Num. obs: 128996 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 9.98 % / Biso Wilson estimate: 33.101 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.113 / Χ2: 1.154 / Net I/σ(I): 14.46 / Num. measured all: 1287351
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.919.591.2881.5119439720785202710.8141.36197.5
1.91-2.0410.40.684320295819543195150.9420.71999.9
2.04-2.210.2880.3935.2218693618192181710.9760.41399.9
2.2-2.419.8560.2657.9616575916831168180.9870.2899.9
2.41-2.6910.470.16212.8215900615196151870.9940.17199.9
2.69-3.119.7940.09921.113217613504134960.9970.10599.9
3.11-3.810.0370.06136.2411486011447114440.9980.064100
3.8-5.369.250.04745.0982893897189610.9990.0599.9
5.36-46.739.4230.03748.5748366514851330.9990.03999.7

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Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQ2

1yq2


Resolution: 1.8→46.73 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1975 / WRfactor Rwork: 0.1611 / FOM work R set: 0.8463 / SU B: 4.859 / SU ML: 0.077 / SU R Cruickshank DPI: 0.0913 / SU Rfree: 0.0948 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 2100 1.6 %RANDOM
Rwork0.1611 ---
obs0.1618 126888 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.5 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 137.02 Å2 / Biso mean: 44.29 Å2 / Biso min: 25.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å2-0 Å2
3----3.58 Å2
Refinement stepCycle: final / Resolution: 1.8→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7610 0 24 1182 8816
Biso mean--66.69 52.74 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197961
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.94610863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58851022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09423.146391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.642151195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.191578
X-RAY DIFFRACTIONr_chiral_restr0.1520.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216345
LS refinement shellResolution: 1.796→1.843 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 146 -
Rwork0.303 8872 -
all-9018 -
obs--94.74 %
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)
10.3234-0.217-0.0660.15520.10420.6298-0.0839-0.022-0.08760.06050.01430.06990.1278-0.15510.06960.1101-0.01630.06640.08690.05290.115721.459327.885440.0291
21.0428-0.16820.13790.0442-0.08931.0741-0.0919-0.17960.06010.03220.08770.00980.30510.2470.00420.19150.18930.01880.19250.02250.026955.248726.561748.4885
30.2834-0.1235-0.05660.06780.07830.5777-0.0147-0.0166-0.00810.02930.02790.02370.06060.0417-0.01330.09450.03830.01110.0240.01270.101942.904134.425724.8374
40.8777-0.6727-0.67530.56550.50650.5309-0.1132-0.05580.01890.11050.1071-0.03130.13780.05850.00610.1950.1319-0.00850.1226-0.02240.035866.549515.011910.5354
50.1401-0.15550.21090.2021-0.16890.73780.07450.077-0.0074-0.0366-0.08620.03290.15810.0790.01170.11650.0569-0.00860.0706-0.04920.099641.611723.0054-12.9647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 224
2X-RAY DIFFRACTION2A225 - 313
3X-RAY DIFFRACTION3A314 - 605
4X-RAY DIFFRACTION4A606 - 713
5X-RAY DIFFRACTION5A714 - 1100

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