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- PDB-6lvw: Polyextremophilic Beta-galactosidase from the Antarctic haloarcha... -

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Basic information

Entry
Database: PDB / ID: 6lvw
TitlePolyextremophilic Beta-galactosidase from the Antarctic haloarchaeon Halorubrum lacusprofundi
ComponentsBeta-galactosidase Bga
KeywordsHYDROLASE / polyextremophilic enzyme / halophile / psychrophile / extremozyme / extremophile / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Beta-galactosidase Bga
Similarity search - Component
Biological speciesHalorubrum lacusprofundi
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsMuhammad, R. / Arold, S.T.
CitationJournal: Microorganisms / Year: 2020
Title: Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme.
Authors: Karan, R. / Mathew, S. / Muhammad, R. / Bautista, D.B. / Vogler, M. / Eppinger, J. / Oliva, R. / Cavallo, L. / Arold, S.T. / Rueping, M.
History
DepositionFeb 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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 Bga
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2263
Polymers78,1361
Non-polymers902
Water543
1
A: Beta-galactosidase Bga
hetero molecules

A: Beta-galactosidase Bga
hetero molecules

A: Beta-galactosidase Bga
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,6789
Polymers234,4093
Non-polymers2696
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area14030 Å2
ΔGint-77 kcal/mol
Surface area62730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.130, 100.130, 137.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Beta-galactosidase Bga / Polyextremophilic Beta-galactosidase / Beta-gal


Mass: 78136.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34) (archaea)
Strain: ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34 / Gene: Hlac_2868 / Production host: Haloferax volcanii (archaea) / References: UniProt: B9LW38, beta-galactosidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 85 mM Tris-HCl (pH 8.5), 142 mM MgCl2, 2.78 M 1,6-hexanediol, 450 mM NDSB-195

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.49→50.07 Å / Num. obs: 27127 / % possible obs: 99.3 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.034 / Rrim(I) all: 0.153 / Net I/σ(I): 15 / Num. measured all: 539186 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.49-2.5615.90.045782979318780.5471.1624.7290.693.2
11.15-50.0716.30.0552023200.9990.0120.0525899

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KWG

1kwg


Resolution: 2.493→34.357 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 44.65
RfactorNum. reflection% reflection
Rfree0.3075 1230 5.21 %
Rwork0.2456 --
obs0.2489 23595 86.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 251.44 Å2 / Biso mean: 100.9852 Å2 / Biso min: 39.8 Å2
Refinement stepCycle: final / Resolution: 2.493→34.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5275 0 2 3 5280
Biso mean--93.92 66.24 -
Num. residues----668
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.493-2.59240.53611100.4814174662
2.5924-2.71030.53531020.4228198669
2.7103-2.85310.41481360.3528217677
2.8531-3.03180.40181230.3472245585
3.0318-3.26570.3761390.3132262692
3.2657-3.5940.30941420.2729274896
3.594-4.11330.31431450.2431285399
4.1133-5.17950.29531590.21212867100
5.1795-34.3570.2651740.21062908100
Refinement TLS params.Method: refined / Origin x: 18.2566 Å / Origin y: 37.2514 Å / Origin z: 2.3014 Å
111213212223313233
T0.6727 Å20.3605 Å20.0491 Å2-0.609 Å2-0.0237 Å2--0.5656 Å2
L1.4473 °20.1849 °2-0.088 °2-0.9273 °2-0.1526 °2--2.728 °2
S0.0682 Å °0.0273 Å °-0.1816 Å °-0.0438 Å °-0.0767 Å °-0.1836 Å °1.0317 Å °0.951 Å °0.0117 Å °
Refinement TLS groupSelection details: all

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