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- PDB-7p01: Structure of the maltase BaAG2 from Blastobotrys adeninivorans in... -

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Basic information

Entry
Database: PDB / ID: 7p01
TitleStructure of the maltase BaAG2 from Blastobotrys adeninivorans in complex with acarbose
ComponentsBaAG2
KeywordsHYDROLASE / Maltase / acarbose / inhibitor / GH13
Function / homologyalpha-acarbose / 1-methylpyrrolidin-2-one
Function and homology information
Biological speciesBlastobotrys adeninivorans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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

Downloads & links

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Assembly

Deposited unit
A: BaAG2
B: BaAG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,97810
Polymers135,6632
Non-polymers2,3148
Water12,196677
1
A: BaAG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3616
Polymers67,8321
Non-polymers1,5305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BaAG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6164
Polymers67,8321
Non-polymers7853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.030, 78.080, 121.930
Angle α, β, γ (deg.)90.000, 94.096, 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: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp4Gc]{[(4+1)][<C2O2>]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MB3 / 1-methylpyrrolidin-2-one


Mass: 99.131 Da / Num. of mol.: 3 / 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.: 677 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
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 EIGER2 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: 2.12→46.32 Å / Num. obs: 140413 / % possible obs: 98.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.97 / Rsym value: 0.23 / Net I/σ(I): 7.68
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.54 / Num. unique obs: 10323 / CC1/2: 0.623 / Rsym value: 1.152 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3aj7

3aj7


Resolution: 2.12→46.32 Å / SU ML: 0.2465 / Cross valid method: FREE R-VALUE / σ(F): 0.87 / Phase error: 22.1306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 2026 2.8 %Random
Rwork0.1842 136415 --
obs0.1846 140350 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.64 Å2
Refinement stepCycle: LAST / Resolution: 2.12→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9345 0 155 677 10177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0199767
X-RAY DIFFRACTIONf_angle_d1.887613269
X-RAY DIFFRACTIONf_chiral_restr0.10071408
X-RAY DIFFRACTIONf_plane_restr0.00921699
X-RAY DIFFRACTIONf_dihedral_angle_d22.28263552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.150.32261350.30674805X-RAY DIFFRACTION98.68
2.15-2.170.33361400.29464859X-RAY DIFFRACTION98.76
2.17-2.20.29521420.28224918X-RAY DIFFRACTION99
2.2-2.230.2831380.2734827X-RAY DIFFRACTION99.18
2.23-2.260.31971410.26594889X-RAY DIFFRACTION98.82
2.26-2.30.26651450.25734971X-RAY DIFFRACTION98.88
2.3-2.330.26861380.25284739X-RAY DIFFRACTION98.27
2.33-2.370.28771410.24654903X-RAY DIFFRACTION99.06
2.37-2.410.23411410.25034861X-RAY DIFFRACTION98.7
2.41-2.460.28391380.25294853X-RAY DIFFRACTION98.73
2.46-2.50.26981410.24134905X-RAY DIFFRACTION98.92
2.5-2.550.26561400.22784835X-RAY DIFFRACTION99.16
2.55-2.610.21861400.22454909X-RAY DIFFRACTION98.84
2.61-2.670.26621420.21164852X-RAY DIFFRACTION99.48
2.67-2.740.23871390.21814922X-RAY DIFFRACTION99
2.74-2.810.22981380.21044872X-RAY DIFFRACTION99.27
2.81-2.890.19151430.20514921X-RAY DIFFRACTION99.1
2.89-2.990.21811450.20534884X-RAY DIFFRACTION99.15
2.99-3.090.20071410.18944895X-RAY DIFFRACTION99.17
3.09-3.220.18971400.194899X-RAY DIFFRACTION99.11
3.22-3.360.17381370.18264823X-RAY DIFFRACTION98.71
3.36-3.540.19241420.17084897X-RAY DIFFRACTION99.06
3.54-3.760.19391420.15634864X-RAY DIFFRACTION98.74
3.76-4.050.16271380.13944868X-RAY DIFFRACTION98.91
4.05-4.460.12921430.12994843X-RAY DIFFRACTION98.64
4.46-5.110.13021470.12064870X-RAY DIFFRACTION98.43
5.11-6.430.1561390.14824879X-RAY DIFFRACTION98.66
6.43-46.320.14571390.15644852X-RAY DIFFRACTION98.71
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)
11.2853035626-0.2228419910410.2594688038011.204853275440.05804454025461.18474970672-0.03711790764630.3727200977910.183418081757-0.3301618707080.03716604872850.0747872111058-0.0963718392817-0.03340505083660.002364064617330.338642033531-0.0423602846546-0.02242269253610.2803487858340.07839830293860.300726219897-26.0688061634-3.66085692179-22.2581579963
21.132168804520.06313654114010.1669432606340.9372864783070.04445468786260.761249724678-0.04318124213710.235127797024-0.00724417206565-0.1742962212720.105479731142-0.04383365627410.0528735132816-0.00721898287678-0.0675881831430.273672950307-0.030270752469-0.002667624445280.214979019418-0.002470410490490.256315630628-21.0579517048-15.3037856321-14.1678028855
32.78109648293-0.705158158716-0.07076824312662.03796227154-0.6669393739521.9754997788-0.0543857175721-0.0332914549815-0.1663930794640.02585940374380.0904813633808-0.3526208225760.1723738753450.101064483764-0.04810185737580.237081203467-0.00491779162719-0.05909424321280.173382898525-0.04444185001480.30135082011-4.42747041178-24.36603837723.32927810252
44.7741437281-0.0286548510211.065136052580.803794818310.1475844453633.422153734010.01453581179370.227705001628-0.0486692709871-0.147406997452-0.01299391167720.139301303917-0.0440820314444-0.2240091217660.0266677924550.376586333575-0.0289979351076-0.09356741366570.302859908668-0.002542128181820.287188092978-6.22884442739-40.5823757535-31.5159741741
51.70744067717-0.07988892649770.7975608793750.6126661024650.4353727769043.131833611660.1703457124740.853832091954-0.0735246292212-0.370444653469-0.1277024398770.119612639605-0.07458619167630.0215661237627-0.05509011047930.5793064124710.105256246745-0.1397374918910.735639821853-0.006245793464110.34742756104-7.71098506829-37.2138486083-52.7213699133
61.78330593028-0.5391132163810.3019616390191.32884140408-0.2225702374481.627548700180.1654518859720.563582247754-0.417729077309-0.378978687495-0.1018430458650.2061910729550.2885549991390.0390451432376-0.0571514424820.4664374028-0.00160802165876-0.1199129246040.443711552796-0.0974324965450.3275935320994.49613403741-52.0155393261-38.0795401834
74.18606485616-1.34098854324-0.1697753262793.38337166113-1.691547319183.279791913340.03649369991570.3855432673750.0441398774434-0.15992879633-0.169911286495-0.4318022863560.221887624580.4998010770490.1241616448170.340122983788-0.0152534757719-0.06959140660980.364620607073-0.01857183400470.2617954825724.9532015641-50.4151617815-27.8435004838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 190 )
2X-RAY DIFFRACTION2chain 'A' and (resid 191 through 484 )
3X-RAY DIFFRACTION3chain 'A' and (resid 485 through 581 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 88 )
5X-RAY DIFFRACTION5chain 'B' and (resid 89 through 262 )
6X-RAY DIFFRACTION6chain 'B' and (resid 263 through 484 )
7X-RAY DIFFRACTION7chain 'B' and (resid 485 through 581 )

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