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- PDB-8xc9: Amylase A in complex with acarbose -

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Basic information

Entry
Database: PDB / ID: 8xc9
TitleAmylase A in complex with acarbose
ComponentsAmyA
KeywordsHYDROLASE
Function / homologyacarbose-derived trisaccharide
Function and homology information
Biological speciesAlkalimonas delamerensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsZhao, F. / Xu, T.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of amylase AmyA in complex with acarbose.
Authors: Zhao, F. / Xu, T.T.
History
DepositionDec 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmyA
B: AmyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0754
Polymers113,1082
Non-polymers9672
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.000, 140.000, 84.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein AmyA


Mass: 56554.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalimonas delamerensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#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


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 483.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: acarbose-derived trisaccharide
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp4Gc]{[(4+1)][<C2O2>]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium iodide, 0.1 M BIS-Tris Propane (pH 7.5), 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.89→36.43 Å / Num. obs: 75774 / % possible obs: 99.6 % / Redundancy: 17.2 % / CC1/2: 0.998 / Net I/σ(I): 14
Reflection shellResolution: 1.89→1.94 Å / Num. unique obs: 5369 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→36.43 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 2004 2.65 %
Rwork0.2209 --
obs0.2221 75708 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7436 0 66 552 8054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077701
X-RAY DIFFRACTIONf_angle_d0.79210523
X-RAY DIFFRACTIONf_dihedral_angle_d8.3891015
X-RAY DIFFRACTIONf_chiral_restr0.051042
X-RAY DIFFRACTIONf_plane_restr0.0061382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.36841370.32165023X-RAY DIFFRACTION96
1.94-1.990.4191380.31235164X-RAY DIFFRACTION98
1.99-2.050.36111430.30365198X-RAY DIFFRACTION99
2.05-2.110.32881390.27485213X-RAY DIFFRACTION100
2.11-2.190.35851470.26955275X-RAY DIFFRACTION100
2.19-2.280.34461460.26245261X-RAY DIFFRACTION100
2.28-2.380.3261390.2565263X-RAY DIFFRACTION100
2.38-2.510.34991420.26035263X-RAY DIFFRACTION100
2.51-2.660.31211410.25445263X-RAY DIFFRACTION100
2.66-2.870.29441420.24025290X-RAY DIFFRACTION100
2.87-3.160.25351470.22745299X-RAY DIFFRACTION100
3.16-3.610.23191500.19425331X-RAY DIFFRACTION100
3.61-4.550.17771470.15785346X-RAY DIFFRACTION100
4.55-36.430.20341460.17435515X-RAY DIFFRACTION100

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