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- PDB-7p07: Structure of the maltase BaAG2 from Blastobotrys adeninivorans in... -

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Basic information

Entry
Database: PDB / ID: 7p07
TitleStructure of the maltase BaAG2 from Blastobotrys adeninivorans in complex with glucose
ComponentsBaAG2
KeywordsHYDROLASE / Maltase / glucose / GH13 / alpha-glucosidase
Function / homologyalpha-D-glucopyranose / 1-methylpyrrolidin-2-one
Function and homology information
Biological speciesBlastobotrys adeninivorans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.13 Å
AuthorsErnits, K. / Visnapuu, T. / Persson, K.
Funding support Sweden, Estonia, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Other privateJCK-1918 Sweden
Estonian Research CouncilPUT1050 Estonia
Citation
Journal: J Fungi (Basel) / Year: 2021
Title: Structural Insight into a Yeast Maltase-The Ba AG2 from Blastobotrys adeninivorans with Transglycosylating Activity.
Authors: Ernits, K. / Kjeldsen, C. / Persson, K. / Grigor, E. / Alamae, T. / Visnapuu, T.
#1: Journal: J Fungi / Year: 2021
Title: Structural Insight into a Yeast Maltase-The BaAG2 from Blastobotrys adeninivorans with Transglycosylating Activity
Authors: Ernits, K. / Kjeldsen, C. / Persson, K. / Grigor, E. / Alamae, T. / Visnapuu, T.
History
DepositionJun 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BaAG2
B: BaAG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,3028
Polymers135,6632
Non-polymers6396
Water6,756375
1
A: BaAG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1514
Polymers67,8321
Non-polymers3193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BaAG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1514
Polymers67,8321
Non-polymers3193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.880, 77.730, 121.110
Angle α, β, γ (deg.)90.000, 92.900, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein BaAG2


Mass: 67831.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastobotrys adeninivorans (fungus) / Plasmid: pURI3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: alpha-glucosidase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MB3 / 1-methylpyrrolidin-2-one


Mass: 99.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M MES (pH 5.5) 12% polyvinylpyrrolidone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979965 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979965 Å / Relative weight: 1
ReflectionResolution: 2.13→47.73 Å / Num. obs: 134791 / % possible obs: 98.9 % / Redundancy: 3.55 % / Biso Wilson estimate: 42.14 Å2 / CC1/2: 0.998 / Rsym value: 0.097 / Net I/σ(I): 8.61
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 3.58 % / Mean I/σ(I) obs: 1.19 / Num. unique obs: 10026 / CC1/2: 0.7 / Rsym value: 1.204 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7P01

7p01


Resolution: 2.13→47.73 Å / SU ML: 0.2945 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 30.0735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 2016 2.9 %
Rwork0.215 130659 -
obs0.2154 134563 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.58 Å2
Refinement stepCycle: LAST / Resolution: 2.13→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9355 0 40 375 9770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01679654
X-RAY DIFFRACTIONf_angle_d1.889913099
X-RAY DIFFRACTIONf_chiral_restr0.16931362
X-RAY DIFFRACTIONf_plane_restr0.00921700
X-RAY DIFFRACTIONf_dihedral_angle_d22.4773539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.160.38891420.40964742X-RAY DIFFRACTION99.15
2.16-2.180.35311360.38024639X-RAY DIFFRACTION98.64
2.18-2.210.36611420.37184659X-RAY DIFFRACTION98.04
2.21-2.240.39251400.35214632X-RAY DIFFRACTION98.47
2.24-2.270.35921400.34334645X-RAY DIFFRACTION98.58
2.27-2.310.30121380.34054704X-RAY DIFFRACTION98.88
2.31-2.340.36651350.32144643X-RAY DIFFRACTION98.98
2.34-2.380.37151430.31254728X-RAY DIFFRACTION99.21
2.38-2.420.35291410.30284649X-RAY DIFFRACTION99.32
2.42-2.470.27611400.29844709X-RAY DIFFRACTION98.98
2.47-2.520.28861390.28984647X-RAY DIFFRACTION98.78
2.52-2.570.30981400.28964749X-RAY DIFFRACTION99.03
2.57-2.620.30651420.28954587X-RAY DIFFRACTION98.79
2.62-2.680.27541410.27874670X-RAY DIFFRACTION98.08
2.68-2.750.27741370.26864597X-RAY DIFFRACTION98.4
2.75-2.830.21211410.2564716X-RAY DIFFRACTION98.38
2.83-2.910.27051340.25524607X-RAY DIFFRACTION98.24
2.91-30.23861410.24894679X-RAY DIFFRACTION98.79
3-3.110.29041380.24264660X-RAY DIFFRACTION98.6
3.11-3.230.26881390.23864641X-RAY DIFFRACTION98.62
3.23-3.380.25091420.22254683X-RAY DIFFRACTION98.83
3.38-3.560.25291390.19854695X-RAY DIFFRACTION99.1
3.56-3.780.22651380.18184668X-RAY DIFFRACTION98.85
3.78-4.070.20581410.16894641X-RAY DIFFRACTION98.68
4.07-4.480.15981430.15034711X-RAY DIFFRACTION98.76
4.48-5.130.16211380.1434653X-RAY DIFFRACTION98.4
5.13-6.460.15731350.16774638X-RAY DIFFRACTION98.84
6.46-47.730.1781390.16424667X-RAY DIFFRACTION98.83
Refinement TLS params.Method: refined / Origin x: -9.21369827651 Å / Origin y: -28.8525112479 Å / Origin z: -26.6536625654 Å
111213212223313233
T0.424601395726 Å2-0.0213212729293 Å2-0.201683468018 Å2-0.281473447778 Å20.0178679972803 Å2--0.429714618773 Å2
L0.728675905911 °2-0.085745367087 °2-0.0217187523549 °2-0.312513507328 °20.24818101996 °2--0.705692526697 °2
S-0.0206863211526 Å °0.236324281632 Å °0.0353927735139 Å °-0.125114198059 Å °-0.0659774873526 Å °0.103438590227 Å °-0.12806340871 Å °-0.037025996548 Å °0.0718161845281 Å °
Refinement TLS groupSelection details: all

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