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

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Basic information

Entry
Database: PDB / ID: 6zjw
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant D207A in complex with galactose
ComponentsBeta-galactosidase
KeywordsHYDROLASE / galactosidase / cold-adapted / psychrophilic / dimeric / mutant / loss of function
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 domain-like / Galactose-binding-like domain superfamily / Distorted Sandwich / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.119 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)110,0813
Polymers109,7201
Non-polymers3602
Water5,459303
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,1626
Polymers219,4412
Non-polymers7214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5650 Å2
ΔGint3 kcal/mol
Surface area70520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.284, 139.284, 127.816
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: 109720.438 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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 62.29 %
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: May 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.11→43.863 Å / Num. obs: 81346 / % possible obs: 98.8 % / Redundancy: 5.433 % / Biso Wilson estimate: 45.39 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.199 / Χ2: 1.252 / Net I/σ(I): 5.18 / Num. measured all: 441940
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
2.11-2.245.2141.8060.546484713189124370.6832.00694.3
2.24-2.395.4131.2280.856690712377123600.8341.3699.9
2.39-2.585.8860.8531.46790511539115370.8930.936100
2.58-2.835.770.5392.456137510641106360.9360.592100
2.83-3.165.4920.3394.5252962968396430.9590.37699.6
3.16-3.655.1610.1898.4543987856685230.9820.21199.5
3.65-4.465.420.12313.2139268726272450.990.13699.8
4.46-6.284.8820.09815.4927700571756740.990.10999.2
6.28-43.8635.1620.06919.0816989333332910.9950.07798.7

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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: 2.119→43.863 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2084 2.58 %
Rwork0.2225 78826 -
obs0.2234 80910 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.73 Å2 / Biso mean: 58.6279 Å2 / Biso min: 32.15 Å2
Refinement stepCycle: final / Resolution: 2.119→43.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7607 0 24 303 7934
Biso mean--93.59 46.94 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037854
X-RAY DIFFRACTIONf_angle_d0.59910713
X-RAY DIFFRACTIONf_chiral_restr0.0471145
X-RAY DIFFRACTIONf_plane_restr0.0041436
X-RAY DIFFRACTIONf_dihedral_angle_d11.5474617
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1193-2.16860.41821360.4028515198
2.1686-2.22280.4131360.3693515599
2.2228-2.28290.37011380.3557522999
2.2829-2.350.39681360.3293516999
2.35-2.42590.34561370.3243524199
2.4259-2.51260.36291390.306521599
2.5126-2.61320.35861390.28915224100
2.6132-2.73210.28061380.29755273100
2.7321-2.87610.3051390.26715252100
2.8761-3.05630.31821390.2575261100
3.0563-3.29220.29171390.249524599
3.2922-3.62330.28741400.20845267100
3.6233-4.14730.22521420.18435337100
4.1473-5.22380.15121410.15345334100
5.2238-43.8630.20811450.1766547399
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)
11.0944-0.1505-0.05430.47910.03011.0803-0.0341-0.1792-0.16620.13670.09570.09320.2319-0.126-0.0490.52830.03460.02540.39390.060.405837.717732.081535.0704
20.9151-0.5890.4420.578-0.23230.68740.11030.196-0.1717-0.0889-0.080.10110.29020.1405-0.03340.59370.0683-0.01940.4391-0.05830.468147.495321.6282-5.1269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 567 )A22 - 567
2X-RAY DIFFRACTION2chain 'A' and (resid 568 through 1010 )A568 - 1010

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