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

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Basic information

Entry
Database: PDB / ID: 6zjv
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant D207A
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. / 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
MALONATE ION / beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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)109,8222
Polymers109,7201
Non-polymers1021
Water2,558142
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,6454
Polymers219,4412
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4440 Å2
ΔGint-6 kcal/mol
Surface area69620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.451, 139.451, 127.877
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: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 7.5 / Details: 28% TacsimateTM pH 7.5

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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: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.246→47.125 Å / Num. obs: 68473 / % possible obs: 99.6 % / Redundancy: 20.028 % / Biso Wilson estimate: 49.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.114 / Χ2: 0.794 / Net I/σ(I): 21.38
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
2.25-2.3819.951.8011.5221581410963108180.9181.84898.7
2.38-2.5520.8771.1452.5121597510349103450.9611.173100
2.55-2.7519.8080.7284.05191329966496590.980.74799.9
2.75-3.0120.6190.378.27182495888888510.9940.37999.6
3.01-3.3620.7640.16818.09167299807180570.9990.17399.8
3.36-3.8819.6260.08834.38140015717471340.9990.0999.4
3.88-4.7519.9340.04958.911208396084606210.0599.6
4.75-6.6818.3810.04168.31876214776476710.04299.8
6.68-47.12517.9820.03484.82499722796277910.03599.4

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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: 2.25→47.125 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1094 1.6 %
Rwork0.2362 67127 -
obs0.2365 68221 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 231.46 Å2 / Biso mean: 75.7176 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.25→47.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7604 0 7 142 7753
Biso mean--87.67 73.12 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047916
X-RAY DIFFRACTIONf_angle_d0.88610805
X-RAY DIFFRACTIONf_chiral_restr0.0541146
X-RAY DIFFRACTIONf_plane_restr0.0081456
X-RAY DIFFRACTIONf_dihedral_angle_d6.9866343
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.34790.45591320.403813397
2.3479-2.47170.39561360.3454829799
2.4717-2.62650.35171360.31728383100
2.6265-2.82930.35971360.2963829999
2.8293-3.1140.3351370.29358406100
3.114-3.56440.2611370.2541842999
3.5644-4.49030.22231380.2005846499
4.4903-47.1250.20741420.18788716100
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)
11.5462-0.21-0.19590.595-0.13082.3756-0.0587-0.1349-0.14410.19460.19590.15080.2306-0.17100.75120.11510.04620.42070.070.61838.021432.765735.1643
21.0808-0.21060.011.42490.04552.1009-0.01320.2173-0.08110.14260.03070.08860.62810.42880.00010.96240.3021-0.03870.6486-0.06510.617557.540218.658812.2867
31.6505-0.51720.40870.6783-0.75992.38180.27990.641-0.2397-0.149-0.15480.08850.53660.3130.00430.8560.2189-0.07330.8219-0.16890.686543.198824.0228-12.4066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 563 )A22 - 563
2X-RAY DIFFRACTION2chain 'A' and (resid 564 through 701 )A564 - 701
3X-RAY DIFFRACTION3chain 'A' and (resid 702 through 1010 )A702 - 1010

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