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- PDB-24zq: The alpha amylase AmyY complexed with an acarbose-derived trisacc... -

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Basic information

Entry
Database: PDB / ID: 24zq
TitleThe alpha amylase AmyY complexed with an acarbose-derived trisaccharide.
ComponentsAlpha-amylase
KeywordsHYDROLASE
Function / homologyacarbose-derived trisaccharide
Function and homology information
Biological speciesAlkalimonas sp. NCh-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhao, F. / Xu, T.T. / Chen, X.L. / Zhang, Y.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The alpha amylase AmyY complexed with an acarbose-derived trisaccharide.
Authors: Zhao, F. / Xu, T.T. / Chen, X.L. / Zhang, Y.Z.
History
DepositionMar 25, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: 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
B: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1559
Polymers113,4172
Non-polymers1,7387
Water12,178676
1
A: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5964
Polymers56,7081
Non-polymers8883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-3 kcal/mol
Surface area17230 Å2
MethodPISA
2
B: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5585
Polymers56,7081
Non-polymers8504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.207, 140.207, 84.034
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 Alpha-amylase


Mass: 56708.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalimonas sp. NCh-2 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#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 natural 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: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.1→70.1 Å / Num. obs: 55744 / % possible obs: 100 % / Redundancy: 15.2 % / CC1/2: 0.999 / Net I/σ(I): 17.5
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 61241 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→70.1 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 1836 3.63 %
Rwork0.1887 --
obs0.1901 50627 90.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→70.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7466 0 117 676 8259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077858
X-RAY DIFFRACTIONf_angle_d0.88410741
X-RAY DIFFRACTIONf_dihedral_angle_d15.3831088
X-RAY DIFFRACTIONf_chiral_restr0.0541080
X-RAY DIFFRACTIONf_plane_restr0.0061396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.31971350.26213440X-RAY DIFFRACTION84
2.16-2.220.3141170.25923247X-RAY DIFFRACTION80
2.22-2.290.48041000.36692590X-RAY DIFFRACTION64
2.29-2.370.23161380.23033629X-RAY DIFFRACTION89
2.37-2.470.28641420.21823737X-RAY DIFFRACTION91
2.47-2.580.2741370.21093747X-RAY DIFFRACTION92
2.58-2.720.2871520.21263884X-RAY DIFFRACTION94
2.72-2.890.26791480.20963912X-RAY DIFFRACTION95
2.89-3.110.23761560.21743995X-RAY DIFFRACTION97
3.11-3.420.23041460.18354068X-RAY DIFFRACTION98
3.42-3.920.19671540.16374060X-RAY DIFFRACTION98
3.92-4.930.16061530.13364174X-RAY DIFFRACTION100
4.94-36.470.17231580.15374308X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.5705 Å / Origin y: 45.2767 Å / Origin z: 16.4718 Å
111213212223313233
T0.14 Å2-0.0206 Å20.0144 Å2-0.1477 Å2-0.0104 Å2--0.1537 Å2
L0.0743 °2-0.0965 °20.0086 °2-0.0817 °2-0.0477 °2--0.1 °2
S0.0211 Å °-0.035 Å °0.0238 Å °-0.0059 Å °-0.0018 Å °0.0228 Å °0.0037 Å °-0.0035 Å °0 Å °
Refinement TLS groupSelection details: all

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