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- PDB-9x81: Crystal structure of the C-terminal of an alpha-amylase family gl... -

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Basic information

Entry
Database: PDB / ID: 9x81
TitleCrystal structure of the C-terminal of an alpha-amylase family glycosyl hydrolase from Vibrio parahaemolyticus
ComponentsAlpha-amylase
KeywordsHYDROLASE / alpha-amylase / glycosyl hydrolase
Function / homology
Function and homology information


carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glucodextranase-like, C-terminal / C-terminal binding-module, SLH-like, of glucodextranase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsCheng, Q. / Li, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32202987 China
CitationJournal: To Be Published
Title: Crystal structure of the C-terminal of an alpha-amylase family glycosyl hydrolase from Vibrio parahaemolyticus
Authors: Cheng, Q. / Li, B.
History
DepositionOct 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7544
Polymers33,6141
Non-polymers1413
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-17 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.700, 67.830, 86.210
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: 33613.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: HKB16_09485 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7Y0SH31
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 20 % w/v PEG 6000, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.42→22.5 Å / Num. obs: 53585 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC1/2: 0.999 / Net I/σ(I): 16.3
Reflection shellResolution: 1.42→1.46 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3925 / CC1/2: 0.571

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→22 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.182 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21144 2556 4.8 %RANDOM
Rwork0.17639 ---
obs0.17796 50962 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.732 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0 Å2
2--0.13 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.42→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 8 188 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122432
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162186
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.7653324
X-RAY DIFFRACTIONr_angle_other_deg0.6751.7535049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8265310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.65857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08910364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8811.8311243
X-RAY DIFFRACTIONr_mcbond_other1.8761.8311243
X-RAY DIFFRACTIONr_mcangle_it2.7983.2821552
X-RAY DIFFRACTIONr_mcangle_other2.8023.2841553
X-RAY DIFFRACTIONr_scbond_it3.0092.081189
X-RAY DIFFRACTIONr_scbond_other3.0092.081190
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5093.681773
X-RAY DIFFRACTIONr_long_range_B_refined5.30420.252650
X-RAY DIFFRACTIONr_long_range_B_other5.29719.232618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 209 -
Rwork0.266 3697 -
obs--99.95 %

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