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- PDB-24zp: The alpha amylase AmyY -

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Basic information

Entry
Database: PDB / ID: 24zp
TitleThe alpha amylase AmyY
Componentsalpha amylase
KeywordsHYDROLASE / amylase
Biological speciesAlkalimonas sp. NCh-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
Authors: Zhao, F. / Xu, T.T.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2354
Polymers56,7081
Non-polymers5273
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration analysis showed that AmyY is a monomer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-0 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.441, 71.376, 146.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein alpha amylase


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


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium fluoride, 0.1 M Bis-Tris propane, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→49.44 Å / Num. obs: 83330 / % possible obs: 99 % / Redundancy: 8.9 % / CC1/2: 0.993 / Net I/σ(I): 14.3
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 5.9 % / Num. unique obs: 3678 / CC1/2: 0.969 / % possible all: 90.3

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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: 1.5→35.53 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1704 1999 2.4 %
Rwork0.1492 --
obs0.1497 83248 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 35 759 4527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053913
X-RAY DIFFRACTIONf_angle_d1.0385348
X-RAY DIFFRACTIONf_dihedral_angle_d15.006532
X-RAY DIFFRACTIONf_chiral_restr0.115530
X-RAY DIFFRACTIONf_plane_restr0.006699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.1821300.15515259X-RAY DIFFRACTION91
1.53-1.580.19041370.14575588X-RAY DIFFRACTION96
1.58-1.620.16481410.14365729X-RAY DIFFRACTION99
1.62-1.680.16951410.1445756X-RAY DIFFRACTION99
1.68-1.730.16141430.14935813X-RAY DIFFRACTION99
1.73-1.80.17941410.14655765X-RAY DIFFRACTION100
1.8-1.890.18481440.14825835X-RAY DIFFRACTION100
1.89-1.990.16511440.15515839X-RAY DIFFRACTION100
1.99-2.110.16421430.14555809X-RAY DIFFRACTION100
2.11-2.270.18341450.14985865X-RAY DIFFRACTION100
2.27-2.50.19231440.15525883X-RAY DIFFRACTION100
2.5-2.860.15891460.16035923X-RAY DIFFRACTION100
2.86-3.610.16341470.14735993X-RAY DIFFRACTION100
3.61-35.530.1631530.1436192X-RAY DIFFRACTION100

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