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- PDB-6se9: Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB muta... -

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Basic information

Entry
Database: PDB / ID: 6se9
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant E441Q in complex with lactose bound in shallow mode
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. / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-lactose / ACETATE ION / FORMIC ACID / beta-D-fructofuranose / beta-D-galactopyranose / MALONATE ION / Beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.965 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 / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
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)110,95811
Polymers109,7631
Non-polymers1,19510
Water7,206400
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,91722
Polymers219,5272
Non-polymers2,39020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area9070 Å2
ΔGint-40 kcal/mol
Surface area69050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.902, 138.902, 127.875
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 , 1 types, 1 molecules A

#1: Protein Beta-galactosidase


Mass: 109763.461 Da / Num. of mol.: 1 / Mutation: E441Q
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

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


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
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: 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, 406 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MLI / MALONATE ION


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


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: /psfhome/maria/data/441_lac_fru 35% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.96→47.039 Å / Num. obs: 100927 / % possible obs: 99.5 % / Redundancy: 10.115 % / Biso Wilson estimate: 38.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.113 / Χ2: 1.266 / Net I/σ(I): 14.43 / Num. measured all: 1020829
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
1.96-2.0810.2852.172116203716208157550.8292.28697.2
2.08-2.2310.1831.2831.7315572415299152930.9161.351100
2.23-2.4110.1530.7682.8314470514272142530.9650.80999.9
2.41-2.6310.3560.4634.7713577413114131110.9830.488100
2.63-2.9410.0020.2338.8411931911948119290.9940.24699.8
2.94-3.410.3820.10519.6610941510540105390.9980.11100
3.4-4.169.8530.05338.6188331897389650.9990.05699.9
4.16-5.859.550.03755.7867072703170230.9990.03999.9
5.85-47.0399.4730.0364.25384524072405910.03199.7

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Processing

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

6etz


Resolution: 1.965→47.039 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.76
RfactorNum. reflection% reflection
Rfree0.2381 2091 2.08 %
Rwork0.202 --
obs0.2027 100462 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 171.14 Å2 / Biso mean: 70.9557 Å2 / Biso min: 39.62 Å2
Refinement stepCycle: final / Resolution: 1.965→47.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7606 0 79 400 8085
Biso mean--103.78 57.65 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037894
X-RAY DIFFRACTIONf_angle_d0.60210765
X-RAY DIFFRACTIONf_chiral_restr0.0461156
X-RAY DIFFRACTIONf_plane_restr0.0041437
X-RAY DIFFRACTIONf_dihedral_angle_d15.724598
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.965-2.01040.46111290.4592605892
2.0104-2.06070.45711380.4061649899
2.0607-2.11640.40851370.3693649599
2.1164-2.17870.36021390.3301651199
2.1787-2.2490.33731380.2974655399
2.249-2.32940.27221390.2723651799
2.3294-2.42260.29171390.2588653199
2.4226-2.53290.25011390.2416654599
2.5329-2.66640.25291410.23716593100
2.6664-2.83340.28141400.2292656399
2.8334-3.05220.28341390.23456598100
3.0522-3.35930.23911410.20786630100
3.3593-3.84520.21851420.1746667100
3.8452-4.84370.15851430.13176709100
4.8437-47.0390.2081470.166903100
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)
11.1594-0.3023-0.01840.5952-0.09662.111-0.0748-0.1432-0.24230.1910.16420.12740.3555-0.1015-0.0910.79640.08930.04960.44850.05510.487137.666732.208934.8947
23.6718-1.0518-0.50640.95240.13251.1869-0.05990.2444-0.22990.13510.0217-0.01680.57570.40310.04131.03420.2876-0.02720.6654-0.07110.533558.347818.412412.3718
31.4274-0.26130.76670.1489-0.32953.32780.37580.435-0.3077-0.2007-0.18440.09080.65650.3209-0.21181.02530.2299-0.08660.8089-0.17440.595743.638122.0294-15.1543
41.2022-0.36710.40420.8452-0.29741.9950.24830.4755-0.3089-0.2247-0.1194-0.00050.6330.4083-0.10210.86010.1779-0.06860.8006-0.17450.563142.679923.9266-11.4907
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 701 )A568 - 701
3X-RAY DIFFRACTION3chain 'A' and (resid 702 through 780 )A702 - 780
4X-RAY DIFFRACTION4chain 'A' and (resid 781 through 1010 )A781 - 1010

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