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

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Basic information

Entry
Database: PDB / ID: 6zjq
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant E517Q in complex with galactose
ComponentsBeta-galactosidase
KeywordsHYDROLASE / galactosidase / cold-adapted / psychrophilic / dimeric / mutant / loss of function / galactose
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. ...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. / Beta-galactosidase; Chain A, domain 5 - #10 / 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 / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Distorted Sandwich / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / beta-D-galactopyranose / MALONATE ION / Beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 ?-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)112,28934
Polymers110,0211
Non-polymers2,26833
Water11,187621
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,57868
Polymers220,0412
Non-polymers4,53766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16490 Å2
ΔGint-85 kcal/mol
Surface area67520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.608, 138.608, 127.656
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 / Sugars , 2 types, 3 molecules A

#1: Protein Beta-galactosidase


Mass: 110020.703 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
#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: isolated from a genetically manipulated source
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 , 4 types, 652 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
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: 0.9814 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 1.699→43.724 Å / Num. obs: 155102 / % possible obs: 99.8 % / Redundancy: 10.186 % / Biso Wilson estimate: 28.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.136 / Χ2: 1.169 / Net I/σ(I): 13.47
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
1.7-1.810.3873.6210.6325640424955246860.2973.80998.9
1.8-1.9310.1871.9151.2423863223431234260.5992.017100
1.93-2.089.8210.8972.6221411021808218020.8610.947100
2.08-2.2810.50.4735.1221177520172201690.9540.497100
2.28-2.5510.0920.2878.2918433718266182660.980.302100
2.55-2.9410.3710.14815.616775616177161760.9950.156100
2.94-3.610.2340.06533.3314028113708137080.9990.069100
3.6-5.079.9720.03557.9910694710725107250.9990.037100
5.07-43.7249.7070.02865.4259642615861440.9990.0399.8

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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: 1.7→43.724 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 2100 1.35 %
Rwork0.1645 152977 -
obs0.165 155077 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.9 Å2 / Biso mean: 37.802 Å2 / Biso min: 20.75 Å2
Refinement stepCycle: final / Resolution: 1.7→43.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7595 0 151 621 8367
Biso mean--55.17 48.31 -
Num. residues----987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097947
X-RAY DIFFRACTIONf_angle_d0.97710813
X-RAY DIFFRACTIONf_chiral_restr0.0621145
X-RAY DIFFRACTIONf_plane_restr0.0081468
X-RAY DIFFRACTIONf_dihedral_angle_d10.9784627
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.73830.37421350.3656987297
1.7383-1.78180.35751390.322610115100
1.7818-1.830.31621390.299310161100
1.83-1.88380.3121400.268410160100
1.8838-1.94470.26081390.233810136100
1.9447-2.01420.23241390.20410125100
2.0142-2.09480.19221400.174410182100
2.0948-2.19010.19181390.15410168100
2.1901-2.30560.17641400.142810199100
2.3056-2.450.15221400.142910191100
2.45-2.63920.21551400.142410208100
2.6392-2.90470.19831410.145510243100
2.9047-3.32490.17841410.141610268100
3.3249-4.18850.14261420.126710354100
4.1885-43.7240.20541460.173510595100
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)
10.5044-0.37070.15390.3061-0.04830.50640.0292-0.2051-0.27410.14710.12060.17710.0616-0.3853-00.387-0.05190.01180.42920.12320.445419.493928.705837.4138
20.6757-0.15470.09270.3396-0.12770.88970.0201-0.1032-0.10370.07340.05920.03780.0414-0.0348-00.30140.0094-0.00180.23590.02140.29341.448733.418234.2603
30.9838-0.26630.52260.6861-0.14220.90660.14480.2595-0.1445-0.1176-0.0523-0.0770.24420.27590.00020.4070.0837-0.03020.323-0.04480.340659.054819.802811.4028
40.1105-0.07720.11830.28550.02440.17330.20940.3004-0.207-0.1912-0.07020.03510.34050.4082-0.00020.56730.187-0.08680.5174-0.10260.403652.945614.6935-10.6717
51.1508-0.1228-0.09480.6305-0.75690.95950.15670.0890.0037-0.18850.0633-0.0072-0.20720.1404-0.00010.33460.027-0.03740.3411-0.03410.345737.030231.396-9.7831
61.0668-0.25780.3880.6194-0.19771.67790.15620.2246-0.1787-0.0976-0.04370.01470.34190.24350.00720.35850.0718-0.05340.3417-0.09060.339843.807724.2143-11.6063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 114 )A25 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 567 )A115 - 567
3X-RAY DIFFRACTION3chain 'A' and (resid 568 through 690 )A568 - 690
4X-RAY DIFFRACTION4chain 'A' and (resid 691 through 739 )A691 - 739
5X-RAY DIFFRACTION5chain 'A' and (resid 740 through 789 )A740 - 789
6X-RAY DIFFRACTION6chain 'A' and (resid 790 through 1010 )A790 - 1010

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