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- PDB-6sec: Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cBon co... -

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Basic information

Entry
Database: PDB / ID: 6sec
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cBon complex with ONPG
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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
2-nitrophenyl beta-D-galactopyranoside / ACETATE ION / beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.768 Å
AuthorsRutkiewicz, M. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/ST5/00555 Poland
Citation
Journal: Int J Mol Sci / Year: 2019
Title: Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-d-galactosidase fromArthrobactersp. 32cB.
Authors: Rutkiewicz, M. / Bujacz, A. / Wanarska, M. / Wierzbicka-Wos, A. / Cieslinski, H.
#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
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)110,2075
Polymers109,7641
Non-polymers4424
Water2,432135
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,41410
Polymers219,5292
Non-polymers8858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6410 Å2
ΔGint-35 kcal/mol
Surface area67960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.330, 137.330, 126.784
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: 109764.445 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.: 2 / 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: Sugar ChemComp-145 / 2-nitrophenyl beta-D-galactopyranoside / 1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE / 2-nitrophenyl beta-D-galactoside / 2-nitrophenyl D-galactoside / 2-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO8 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
1-O-[O-nitrophenyl]-b-D-galactopyranoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.21 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 35% Tacsimate pH 6.0

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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 PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.59→46.578 Å / Num. obs: 67872 / % possible obs: 99.4 % / Redundancy: 6.625 % / Biso Wilson estimate: 58.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.168 / Χ2: 1.065 / Net I/σ(I): 11.75
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
2.59-2.746.3221.5131.0343053694268100.6251.65198.1
2.74-2.936.8151.0091.7144705656965600.8041.09499.9
2.93-3.167.0340.6053.1142808609860860.9160.65499.8
3.16-3.466.880.3326.1338482561855930.9730.3699.6
3.46-3.876.3190.19410.7532118510450830.9880.21199.6
3.87-4.466.4850.119.4229332453745230.9960.10999.7
4.46-5.456.8260.06827.2826363386938620.9980.07499.8
5.45-7.666.1810.05830.2118722304330290.9980.06399.5
7.66-46.5786.4350.02755.1811467181117820.9990.0398.4

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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: 2.768→46.578 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.24 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 2112 3.11 %
Rwork0.1721 65760 -
obs0.1743 67872 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.11 Å2 / Biso mean: 63.3921 Å2 / Biso min: 19.61 Å2
Refinement stepCycle: final / Resolution: 2.768→46.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7603 0 30 135 7768
Biso mean--70.77 50.7 -
Num. residues----988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087857
X-RAY DIFFRACTIONf_angle_d1.00810714
X-RAY DIFFRACTIONf_chiral_restr0.0561139
X-RAY DIFFRACTIONf_plane_restr0.0061441
X-RAY DIFFRACTIONf_dihedral_angle_d9.0056301
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.768-2.83240.42241340.3238424796
2.8324-2.90320.36281400.2884371100
2.9032-2.98170.33231400.27524390100
2.9817-3.06940.32151410.26234389100
3.0694-3.16850.31621430.2364459100
3.1685-3.28170.26321430.21784383100
3.2817-3.4130.28611390.19744357100
3.413-3.56830.26251410.17214358100
3.5683-3.75640.24581440.17934422100
3.7564-3.99160.23151400.15524386100
3.9916-4.29960.18841390.13364397100
4.2996-4.73190.20151410.12254403100
4.7319-5.41570.18691430.12764380100
5.4157-6.81980.21031460.15224408100
6.8198-46.5780.21811380.15574410100
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)
10.5521-0.22820.03010.10840.13990.9923-0.0421-0.0956-0.0630.11280.11740.01740.2538-0.03180.00280.37640.03870.0220.13360.08160.262436.933331.658335.9329
20.1060.139-0.05790.2286-0.00210.2797-0.1169-0.0320.03910.04690.13620.08120.51780.0719-0.00090.53250.1927-0.0190.2772-0.01860.367854.098719.375713.1624
30.09140.0198-0.01180.0682-0.13790.16190.12450.101-0.0548-0.0065-0.0560.20160.19240.03980.00040.59430.132-0.07180.419-0.07380.412442.147522.8281-14.2269
40.13990.124-0.01550.14250.00980.13330.16030.2032-0.0530.0067-0.09830.03590.27950.098200.49710.1227-0.07110.3449-0.08240.387942.786322.6002-11.5329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 538 )A22 - 538
2X-RAY DIFFRACTION2chain 'A' and (resid 539 through 701 )A539 - 701
3X-RAY DIFFRACTION3chain 'A' and (resid 702 through 789 )A702 - 789
4X-RAY DIFFRACTION4chain 'A' and (resid 790 through 1009 )A790 - 1009

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