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- PDB-6sed: Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB in c... -

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Basic information

Entry
Database: PDB / ID: 6sed
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB in complex with galactose
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. ...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
ACETATE ION / FORMIC ACID / beta-D-galactopyranose / MALONATE ION / Beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.233 Å
AuthorsRutkiewicz, M. / Bujacz, A. / Kaminska, P. / 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 1.2Nov 6, 2019Group: Data collection / Structure summary / Category: audit_author
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 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)110,75918
Polymers109,7641
Non-polymers99517
Water10,899605
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,51836
Polymers219,5292
Non-polymers1,98934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10170 Å2
ΔGint-88 kcal/mol
Surface area68050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.875, 136.875, 126.833
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, 2 molecules A

#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: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
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 , 5 types, 621 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 605 / 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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 40% 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: 2.1→46.516 Å / Num. obs: 80260 / % possible obs: 99.8 % / Redundancy: 10.076 % / Biso Wilson estimate: 37.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.136 / Χ2: 1.216 / Net I/σ(I): 16.07 / Num. measured all: 808666
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
2.1-2.229.6571.3311.7212307512835127440.7221.40699.3
2.22-2.3810.0430.9182.5712148512113120970.8410.96899.9
2.38-2.5710.730.6583.7912085311270112630.9240.69199.9
2.57-2.8110.5380.3976.2510946510397103880.9680.41799.9
2.81-3.149.910.20211.9593664945694510.9910.21499.9
3.14-3.639.8210.09325.2782293838383790.9980.098100
3.63-4.4310.280.05443.0273221712471230.9990.057100
4.43-6.249.4440.04251.4752714558355820.9990.045100
6.24-46.5169.8660.0365.28318963243323310.03299.7

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Processing

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

6etz


Resolution: 2.233→46.516 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.27
RfactorNum. reflection% reflection
Rfree0.2044 2101 3.15 %
Rwork0.1653 --
obs0.1666 66728 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 197.4 Å2 / Biso mean: 48.1031 Å2 / Biso min: 26.98 Å2
Refinement stepCycle: final / Resolution: 2.233→46.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7606 0 65 605 8276
Biso mean--68.62 46.23 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027930
X-RAY DIFFRACTIONf_angle_d0.56310806
X-RAY DIFFRACTIONf_chiral_restr0.0451147
X-RAY DIFFRACTIONf_plane_restr0.0031457
X-RAY DIFFRACTIONf_dihedral_angle_d13.874655
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.233-2.28480.30761380.2585422999
2.2848-2.3420.26661380.254244100
2.342-2.40530.29431380.23964265100
2.4053-2.47610.24841390.22544274100
2.4761-2.5560.26781400.22414291100
2.556-2.64730.28211380.2134270100
2.6473-2.75330.24481400.2114290100
2.7533-2.87860.26961390.20244276100
2.8786-3.03030.24681400.1994313100
3.0303-3.22020.23781390.18434273100
3.2202-3.46870.2121410.15554337100
3.4687-3.81760.16161400.13344321100
3.8176-4.36970.15961410.11364350100
4.3697-5.5040.13331430.11344382100
5.504-46.5160.19461470.16484512100
Refinement TLS params.Method: refined / Origin x: 41.4379 Å / Origin y: 27.1459 Å / Origin z: 17.6278 Å
111213212223313233
T0.421 Å20.0381 Å2-0.0078 Å2-0.2773 Å20.0046 Å2--0.4082 Å2
L0.5161 °2-0.2236 °2-0.0183 °2-0.2916 °2-0.0055 °2--1.0215 °2
S0.0277 Å °0.0393 Å °-0.1196 Å °0.0106 Å °0.0189 Å °0.0811 Å °0.2293 Å °-0.0208 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA22 - 1010
2X-RAY DIFFRACTION1allG1
3X-RAY DIFFRACTION1allW1 - 605
4X-RAY DIFFRACTION1allC1 - 7
5X-RAY DIFFRACTION1allD1
6X-RAY DIFFRACTION1allE1 - 5
7X-RAY DIFFRACTION1allF1 - 3

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