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- PDB-8jn0: N/F domain of alkaline amylase Amy703 -

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Basic information

Entry
Database: PDB / ID: 8jn0
TitleN/F domain of alkaline amylase Amy703
ComponentsAlpha-amylase
KeywordsHYDROLASE / N-terminus domain / CBM48
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process
Similarity search - Function
Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesAlkalihalophilus pseudofirmus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22826373091 Å
AuthorsXiang, L. / Zhang, G. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670069 China
CitationJournal: To Be Published
Title: Truncation of N-terminus domain of alkaline a-amylase to form a unique dimer leads to improved activity and stability and decreased calcium ion dependence
Authors: Xiang, L. / Zhang, G. / Zhou, J.
History
DepositionJun 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase


Theoretical massNumber of molelcules
Total (without water)10,3961
Polymers10,3961
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.045, 45.045, 91.378
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Alpha-amylase


Mass: 10396.456 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalihalophilus pseudofirmus (bacteria)
Gene: amy / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A023I4U3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M CaCl2, 0.1 M Hepes pH 7, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 31184 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 14.6357131513 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 60
Reflection shellResolution: 1.22→1.24 Å / Rmerge(I) obs: 1.085 / Num. unique obs: 1188

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22826373091→21.8680456558 Å / SU ML: 0.145533988506 / Cross valid method: FREE R-VALUE / σ(F): 1.39770961095 / Phase error: 24.8916277645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223181006645 1396 4.88248461108 %
Rwork0.201070263678 27196 -
obs0.202181684497 28592 93.5908346972 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.4852598585 Å2
Refinement stepCycle: LAST / Resolution: 1.22826373091→21.8680456558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms736 0 0 107 843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00739477755506758
X-RAY DIFFRACTIONf_angle_d0.9167432957841031
X-RAY DIFFRACTIONf_chiral_restr0.083742929624104
X-RAY DIFFRACTIONf_plane_restr0.00688565592922137
X-RAY DIFFRACTIONf_dihedral_angle_d17.6562706807277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2283-1.27220.302360743996610.3248024980561127X-RAY DIFFRACTION39.0789473684
1.2722-1.32310.2817981161821610.2640226802112814X-RAY DIFFRACTION96.6536712151
1.3231-1.38330.259025577671690.2364668670562832X-RAY DIFFRACTION99.9666888741
1.3833-1.45620.2479153474261390.2281419596412949X-RAY DIFFRACTION100
1.4562-1.54740.2394615981531360.2225536798372906X-RAY DIFFRACTION100
1.5474-1.66690.2537697535151360.2079196324442917X-RAY DIFFRACTION100
1.6669-1.83450.2374718523611510.2227115560112884X-RAY DIFFRACTION99.9670619236
1.8345-2.09980.2163566062741380.2078017242632908X-RAY DIFFRACTION100
2.0998-2.64480.2104912391271610.1983610422242914X-RAY DIFFRACTION100
2.6448-21.80.2101100033531440.1780615923912945X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.4308736816 Å / Origin y: -4.04841148508 Å / Origin z: -3.73424668653 Å
111213212223313233
T0.122357031355 Å2-0.0126035342863 Å20.0101937997507 Å2-0.0753751771287 Å2-0.0389827797796 Å2--0.129321711946 Å2
L2.02881784301 °2-0.298839303966 °2-0.620429149089 °2-3.03521302332 °20.982859246649 °2--3.35368976652 °2
S0.087437090541 Å °0.0315214771288 Å °-0.10727222365 Å °0.0458558042754 Å °-0.218169584214 Å °0.347779962676 Å °0.0658462658173 Å °-0.0111338677085 Å °0.0907324408349 Å °
Refinement TLS groupSelection details: all

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