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- PDB-8orp: Crystal structure of Drosophila melanogaster alpha-amylase in com... -

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Basic information

Entry
Database: PDB / ID: 8orp
TitleCrystal structure of Drosophila melanogaster alpha-amylase in complex with the inhibitor acarbose
ComponentsAlpha-amylase A
KeywordsHYDROLASE / ALPHA-AMYLASE / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / BETA- ALPHA-EIGHT BARREL / ADAPTATION / INHIBITOR / ACARBOSE
Function / homology
Function and homology information


Digestion of dietary carbohydrate / alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular region
Similarity search - Function
Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
STRONTIUM ION / Alpha-amylase A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsAghajari, N. / Haser, R.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Molecules / Year: 2023
Title: Structural and Functional Characterization of Drosophila melanogaster alpha-Amylase.
Authors: Rhimi, M. / Da Lage, J.L. / Haser, R. / Feller, G. / Aghajari, N.
History
DepositionApr 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-amylase A
B: Alpha-amylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,64150
Polymers107,5952
Non-polymers5,04648
Water15,763875
1
A: Alpha-amylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25824
Polymers53,7971
Non-polymers2,46123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-amylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,38226
Polymers53,7971
Non-polymers2,58525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.080, 72.540, 98.210
Angle α, β, γ (deg.)90.000, 98.410, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain A
d_2ens_1chain B

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNLYSLYSAA1 - 11919 - 137
d_12TYRTYRGLYGLYAA121 - 382139 - 400
d_13ASPASPLEULEUAA384 - 476402 - 494
d_21GLNGLNLYSLYSBB1 - 11919 - 137
d_22TYRTYRGLYGLYBB121 - 382139 - 400
d_23ASPASPLEULEUBB384 - 476402 - 494

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-amylase A / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 53797.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Amy-p, AmyA, CG18730 / Production host: Escherichia (bacteria) / References: UniProt: P08144, alpha-amylase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 647.622 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RC^RCO/7C$3/6O/5O/4O]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-6-deoxy-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 485.481 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RC^RCO/7C$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 919 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sr / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20 % (v/v) PEG monomethyl ether 550, 0.1 M sodium chloride, 0.1 M bicine buffer (pH 9.0) and 10 mM strontium chloride. Soak in a solution containing 10 mM acarbose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2009
RadiationMonochromator: diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→29.6 Å / Num. obs: 75240 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.57 Å2 / CC1/2: 0.993 / Net I/σ(I): 9
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 10118 / CC1/2: 0.778 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→29.57 Å / SU ML: 0.2105 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.9939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 3759 5 %
Rwork0.1741 71397 -
obs0.176 75156 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.94 Å2
Refinement stepCycle: LAST / Resolution: 2→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7314 0 310 873 8497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00357770
X-RAY DIFFRACTIONf_angle_d0.635710482
X-RAY DIFFRACTIONf_chiral_restr0.04611126
X-RAY DIFFRACTIONf_plane_restr0.00641360
X-RAY DIFFRACTIONf_dihedral_angle_d5.9651102
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.461429737109 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.28621360.24112590X-RAY DIFFRACTION99.78
2.03-2.050.28521380.23722625X-RAY DIFFRACTION99.64
2.05-2.080.29441390.22292629X-RAY DIFFRACTION99.75
2.08-2.110.24841380.21752633X-RAY DIFFRACTION99.64
2.11-2.140.28781380.21962614X-RAY DIFFRACTION99.67
2.14-2.170.2371390.2052636X-RAY DIFFRACTION99.71
2.17-2.210.27381380.19972633X-RAY DIFFRACTION99.71
2.21-2.250.23851390.19622640X-RAY DIFFRACTION99.5
2.25-2.290.23311390.18472629X-RAY DIFFRACTION99.89
2.29-2.330.2261390.1952648X-RAY DIFFRACTION99.71
2.33-2.380.20361370.18342592X-RAY DIFFRACTION99.85
2.38-2.430.25751400.18692671X-RAY DIFFRACTION99.93
2.43-2.490.21991390.18142634X-RAY DIFFRACTION99.96
2.49-2.550.23251390.18112647X-RAY DIFFRACTION99.75
2.55-2.620.2461380.17262620X-RAY DIFFRACTION99.78
2.62-2.70.20841400.182665X-RAY DIFFRACTION99.79
2.7-2.780.24481400.17842646X-RAY DIFFRACTION99.89
2.78-2.880.20351390.17482641X-RAY DIFFRACTION99.93
2.88-30.19831390.16162638X-RAY DIFFRACTION99.82
3-3.140.1851390.162647X-RAY DIFFRACTION99.93
3.14-3.30.18351400.1582665X-RAY DIFFRACTION99.89
3.3-3.510.19891400.15692647X-RAY DIFFRACTION99.86
3.51-3.780.17221390.14452659X-RAY DIFFRACTION99.89
3.78-4.160.16481410.14012665X-RAY DIFFRACTION99.89
4.16-4.760.16121410.14282674X-RAY DIFFRACTION99.54
4.76-5.980.19911400.1672676X-RAY DIFFRACTION99.61
5.98-29.570.22531450.19292733X-RAY DIFFRACTION99.24

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