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- PDB-8jjm: X-ray crystal structure of a multifunctional enzyme (Amy63) from ... -

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Basic information

Entry
Database: PDB / ID: 8jjm
TitleX-ray crystal structure of a multifunctional enzyme (Amy63) from Vibrio alginolyticus 63
ComponentsAmy63
KeywordsHYDROLASE / amylase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / calcium ion binding
Similarity search - Function
Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / 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 alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSun, Y.F. / Zhang, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11179012 China
National Basic Research Program of China (973 Program)2011CB710800 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: The novel amylase function of the carboxyl terminal domain of Amy63.
Authors: Sun, Y. / Liu, G. / Liu, G. / Tang, H. / Sun, C. / Zhang, W. / Chen, L.
History
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amy63
B: Amy63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,54212
Polymers112,0122
Non-polymers53110
Water17,439968
1
A: Amy63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2716
Polymers56,0061
Non-polymers2655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-24 kcal/mol
Surface area17760 Å2
MethodPISA
2
B: Amy63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2716
Polymers56,0061
Non-polymers2655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-24 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.785, 55.495, 106.755
Angle α, β, γ (deg.)90.000, 91.290, 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

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Components

#1: Protein Amy63


Mass: 56005.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2UQL4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 968 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 70% MPD, pH8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U110.9792
SYNCHROTRONNFPSS BL19U120.9792
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→35.79 Å / Num. obs: 101586 / % possible obs: 90.73 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1084 / Net I/σ(I): 12.26
Reflection shellResolution: 1.803→1.868 Å / Num. unique obs: 101586 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.79 Å / SU ML: 0.1505 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1919 2007 2.18 %
Rwork0.1608 90197 -
obs0.1615 92204 90.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 24 968 8918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00768202
X-RAY DIFFRACTIONf_angle_d0.912911146
X-RAY DIFFRACTIONf_chiral_restr0.05621078
X-RAY DIFFRACTIONf_plane_restr0.00661434
X-RAY DIFFRACTIONf_dihedral_angle_d6.14361066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.2674660.22833138X-RAY DIFFRACTION44.17
1.85-1.90.28451020.2224213X-RAY DIFFRACTION60.32
1.9-1.950.2431130.2075319X-RAY DIFFRACTION75.17
1.95-2.020.23031420.19946510X-RAY DIFFRACTION92.07
2.02-2.090.22541570.18626937X-RAY DIFFRACTION98.9
2.09-2.170.24471490.187070X-RAY DIFFRACTION99.79
2.17-2.270.22331620.17147105X-RAY DIFFRACTION99.88
2.27-2.390.20371560.16757044X-RAY DIFFRACTION99.94
2.39-2.540.20351620.1667061X-RAY DIFFRACTION99.88
2.54-2.740.19841580.1677100X-RAY DIFFRACTION99.83
2.74-3.010.17921580.16117098X-RAY DIFFRACTION100
3.01-3.450.14291590.15117135X-RAY DIFFRACTION100
3.45-4.340.17411600.12897147X-RAY DIFFRACTION99.85
4.34-35.790.17831630.157320X-RAY DIFFRACTION99.72

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