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

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Basic information

Entry
Database: PDB / ID: 6zjt
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant E441Q in complex with lactulose
ComponentsBeta-galactosidase
KeywordsHYDROLASE / galactosidase / cold-adapted / psychrophilic / dimeric / mutant / loss of function / galactose / complex
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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
lactulose / ACETATE ION / beta-D-galactopyranose / beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsRutkiewicz, M. / Bujacz, A. / Bujacz, G.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/ST5/00555 Poland
Polish National Science Centre2018/28/T/ST5/00233 Poland
Citation
Journal: Int J Mol Sci / Year: 2020
Title: Mapping the Transglycosylation Relevant Sites of Cold-Adapted beta-d-Galactosidase fromArthrobactersp. 32cB.
Authors: Rutkiewicz, M. / Wanarska, M. / Bujacz, A.
#1: Journal: Int J Mol Sci / Year: 2019
Title: Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-D-galactosidase from
Authors: Rutkiewicz, M. / Bujacz, A. / Wanarska, M. / Wierzbicka-Wos, A. / Cieslinski, H.
History
DepositionJun 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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)110,9729
Polymers109,7631
Non-polymers1,2098
Water6,071337
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,94518
Polymers219,5272
Non-polymers2,41816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6480 Å2
ΔGint-49 kcal/mol
Surface area68220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.974, 138.974, 127.699
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-galactosidase


Mass: 109763.461 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

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-fructofuranose / lactulose


Type: oligosaccharide, Oligosaccharide / Class: Water retention / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactulose
DescriptorTypeProgram
DGalpb1-4DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#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

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Non-polymers , 3 types, 341 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 62.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 37% TacsimateTM pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.97→43.793 Å / Num. obs: 100446 / % possible obs: 99.6 % / Redundancy: 5.604 % / Biso Wilson estimate: 44.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.079 / Χ2: 1.196 / Net I/σ(I): 12.14 / Num. measured all: 562868
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
1.97-2.095.6921.5920.89078016133159490.6551.75398.9
2.09-2.235.5450.9431.388418815198151830.8261.04199.9
2.23-2.415.6050.5082.587942314181141690.9340.56199.9
2.41-2.645.9580.2695.067767413052130360.9790.29599.9
2.64-2.955.8150.1369.86895211869118580.9930.1599.9
2.95-3.45.2130.06719.285441210490104380.9980.07599.5
3.4-4.165.6930.04433.1750687890689030.9990.049100
4.16-5.865.2630.03542.1336517698169380.9980.03999.4
5.86-43.7935.0940.03144.920235405639720.9990.03497.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ETZ

6etz


Resolution: 1.97→43.793 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 2096 2.09 %
Rwork0.1946 98036 -
obs0.1952 100132 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.63 Å2 / Biso mean: 61.7058 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.97→43.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7607 0 80 337 8024
Biso mean--58.19 56.53 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097893
X-RAY DIFFRACTIONf_angle_d1.08110769
X-RAY DIFFRACTIONf_chiral_restr0.1191161
X-RAY DIFFRACTIONf_plane_restr0.0061435
X-RAY DIFFRACTIONf_dihedral_angle_d11.5234600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9701-2.01590.4451390.4285647099
2.0159-2.06630.43551380.3872649599
2.0663-2.12220.36661390.3437644699
2.1222-2.18460.33671390.31066493100
2.1846-2.25510.28531370.2882646599
2.2551-2.33570.32371390.26246479100
2.3357-2.42930.26311400.23766530100
2.4293-2.53980.25391380.22166484100
2.5398-2.67370.24511410.21156559100
2.6737-2.84120.25741400.21076544100
2.8412-3.06050.26031400.22286555100
3.0605-3.36840.24551390.1987652799
3.3684-3.85550.20481420.17296629100
3.8555-4.85660.16621410.13656629100
4.8566-43.7930.18621440.1675673198
Refinement TLS params.Method: refined / Origin x: 42.1538 Å / Origin y: 28.3839 Å / Origin z: 17.525 Å
111213212223313233
T0.5622 Å20.0324 Å2-0.0093 Å2-0.4 Å20.0252 Å2--0.5698 Å2
L0.8893 °2-0.4389 °20.1884 °2-0.5128 °2-0.029 °2--1.5564 °2
S0.0538 Å °0.0117 Å °-0.2476 Å °0.0288 Å °0.0438 Å °0.1469 Å °0.3038 Å °-0.0702 Å °0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA22 - 1010
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allB2
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allC2
6X-RAY DIFFRACTION1allD1
7X-RAY DIFFRACTION1allD2
8X-RAY DIFFRACTION1allE2 - 3
9X-RAY DIFFRACTION1allG1
10X-RAY DIFFRACTION1allG2 - 338

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