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- PDB-6y2k: Crystal structure of beta-galactosidase from the psychrophilic Ma... -

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Basic information

Entry
Database: PDB / ID: 6y2k
TitleCrystal structure of beta-galactosidase from the psychrophilic Marinomonas ef1
Componentsbeta-galactosidase
KeywordsHYDROLASE / glycosyl hydrolase / psychrophilic enzyme / hexameric structure / cold adaptation / enzyme kinetics / cooperativity
Function / homology
Function and homology information


Class I glutamine amidotransferase (GATase) domain / Golgi alpha-mannosidase II / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMarinomonas sp. ef1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMangiagalli, M. / Lapi, M. / Maione, S. / Orlando, M. / Brocca, S. / Pesce, A. / Barbiroli, A. / Pucciarelli, S. / Camilloni, C. / Lotti, M.
CitationJournal: Febs J. / Year: 2021
Title: The co-existence of cold activity and thermal stability in an Antarctic GH42 beta-galactosidase relies on its hexameric quaternary arrangement.
Authors: Mangiagalli, M. / Lapi, M. / Maione, S. / Orlando, M. / Brocca, S. / Pesce, A. / Barbiroli, A. / Camilloni, C. / Pucciarelli, S. / Lotti, M. / Nardini, M.
History
DepositionFeb 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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

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Assembly

Deposited unit
A: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,24113
Polymers75,2491
Non-polymers99212
Water17,619978
1
A: beta-galactosidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)457,44578
Polymers451,4946
Non-polymers5,95172
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_667-y+1,-x+1,-z+5/21
crystal symmetry operation11_657-x+y+1,y,-z+5/21
crystal symmetry operation12_557x,x-y,-z+5/21
Buried area46680 Å2
ΔGint-276 kcal/mol
Surface area118330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.332, 133.332, 232.574
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1004-

HOH

21A-1541-

HOH

31A-1658-

HOH

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Components

#1: Protein beta-galactosidase


Mass: 75248.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas sp. ef1 (bacteria) / Production host: Escherichia coli (E. coli) / References: beta-galactosidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / 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: 4 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M NaCl, 100 mM Na-citrate, 2% ethylene imine polymer.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.9→116.29 Å / Num. obs: 96335 / % possible obs: 100 % / Redundancy: 29.4 % / Rmerge(I) obs: 0.255 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 33.6 % / Rmerge(I) obs: 0.674 / Num. unique obs: 3405 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KWG

1kwg


Resolution: 1.9→116.29 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.462 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 4630 5 %RANDOM
Rwork0.1627 ---
obs0.164 87612 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.35 Å2 / Biso mean: 20.48 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å2-0 Å2
3----2.23 Å2
Refinement stepCycle: final / Resolution: 1.9→116.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 62 999 6305
Biso mean--55.32 34.76 -
Num. residues----656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195588
X-RAY DIFFRACTIONr_bond_other_d0.0020.025018
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9487616
X-RAY DIFFRACTIONr_angle_other_deg0.922311656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81423.464280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63115893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3471543
X-RAY DIFFRACTIONr_chiral_restr0.0720.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021208
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 279 -
Rwork0.289 5855 -
all-6134 -
obs--87.59 %

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