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- PDB-6h1p: Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB - da... -

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Basic information

Entry
Database: PDB / ID: 6h1p
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB - data collected at room temperature
ComponentsBeta-galactosidase
KeywordsHYDROLASE / beta-galactosidase / cold-adapted / psychrophilic / dimer / GH 2 family
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. / 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 / 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
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.009 Å
AuthorsRutkiewicz, M. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Center Poland 2016/21/B/ST5/00555 Poland
Citation
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.
#1: 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 bDG from Arthrobacter sp. 32cB
Authors: Rutkiewicz-Krotewicz, M. / Pietrzyk-Brzezinska, A.J. / Wanarska, M. / Cieslinski, H. / Bujacz, A.
History
DepositionJul 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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)107,7912
Polymers107,7681
Non-polymers231
Water54030
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,5834
Polymers215,5372
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area69660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.219, 140.219, 127.995
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 35% Tacsimate pH 8

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.009→44.05 Å / Num. obs: 29030 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rrim(I) all: 0.222 / Net I/σ(I): 7.7
Reflection shellResolution: 3.009→44.05 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ETZ

6etz


Resolution: 3.009→44.047 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.2294 1452 5 %
Rwork0.1815 --
obs0.184 29023 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.21 Å2 / Biso mean: 50.1311 Å2 / Biso min: 18.89 Å2
Refinement stepCycle: final / Resolution: 3.009→44.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7610 0 1 30 7641
Biso mean--78.98 38.28 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047809
X-RAY DIFFRACTIONf_angle_d0.77710647
X-RAY DIFFRACTIONf_chiral_restr0.0311132
X-RAY DIFFRACTIONf_plane_restr0.0041431
X-RAY DIFFRACTIONf_dihedral_angle_d12.7622805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0092-3.11680.30361410.2872682282397
3.1168-3.24150.3691430.263127122855100
3.2415-3.3890.29161450.247827472892100
3.389-3.56760.26391440.229227462890100
3.5676-3.7910.25461440.202627362880100
3.791-4.08350.20511440.179727262870100
4.0835-4.49410.22851460.155727852931100
4.4941-5.14350.18361460.143127732919100
5.1435-6.4770.21741470.16272786293399
6.477-44.0520.17541520.13772878303098

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