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- PDB-8jnx: alkaline amylase Amy703 with truncated of N-terminus domain -

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Basic information

Entry
Database: PDB / ID: 8jnx
Titlealkaline amylase Amy703 with truncated of N-terminus domain
ComponentsAlpha-amylase
KeywordsHYDROLASE / N-terminus domain / Amylase
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 OF4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.20279875112 Å
AuthorsXiang, L. / Zhang, G. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670069 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: N-terminal domain truncation yielded a unique dimer of polysaccharide hydrolase with enhanced enzymatic activity, stability and calcium ion independence.
Authors: Xiang, L. / Hu, X. / Du, C. / Wu, L. / Lu, Z. / Zhou, J. / Zhang, G.
History
DepositionJun 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)75,5193
Polymers75,4391
Non-polymers802
Water00
1
A: Alpha-amylase
hetero molecules

A: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,0396
Polymers150,8782
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2410 Å2
ΔGint-49 kcal/mol
Surface area53810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.307, 171.307, 167.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Alpha-amylase


Mass: 75439.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalihalophilus pseudofirmus OF4 (bacteria)
Gene: amy / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A023I4U3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.7 Å3/Da / Density % sol: 73.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl, pH 7.5, 2.4 M Sodium malonate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 24396 / % possible obs: 98.06 % / Redundancy: 13.7 % / Biso Wilson estimate: 73.3989253842 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 35
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 1955 / CC1/2: 0.779

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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: 3.20279875112→49.4579 Å / SU ML: 0.326204290268 / Cross valid method: NONE / σ(F): 1.33785944841 / Phase error: 22.9440243257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244565093772 1218 5.0938898415 %
Rwork0.207219680113 22693 -
obs0.209187704736 23911 98.0803150252 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.22 Å2
Refinement stepCycle: LAST / Resolution: 3.20279875112→49.4579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5324 0 2 0 5326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001853739216015475
X-RAY DIFFRACTIONf_angle_d0.4834693703557457
X-RAY DIFFRACTIONf_chiral_restr0.042456049223775
X-RAY DIFFRACTIONf_plane_restr0.00334023078009999
X-RAY DIFFRACTIONf_dihedral_angle_d17.51111989783173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2028-3.3310.2927649066711160.2965157084672111X-RAY DIFFRACTION83.879472693
3.331-3.48260.3580008647591430.2796235420542484X-RAY DIFFRACTION99.469897766
3.4826-3.66610.274917655951370.24718058192513X-RAY DIFFRACTION99.9245852187
3.6661-3.89570.2498233808441180.2196187566652556X-RAY DIFFRACTION100
3.8957-4.19640.2716892408531580.1977296953272515X-RAY DIFFRACTION99.8505790064
4.1964-4.61840.2101797797571310.1735492671432553X-RAY DIFFRACTION99.8140572704
4.6184-5.2860.2126860305871460.1672547906372564X-RAY DIFFRACTION99.9262536873
5.286-6.65730.2410380253161350.1990196054392620X-RAY DIFFRACTION99.9637155298
6.6573-6.89460.2112325101021340.2035239598972777X-RAY DIFFRACTION99.6576514892
Refinement TLS params.Method: refined / Origin x: -43.294148996 Å / Origin y: -44.1208899231 Å / Origin z: -4.91980638074 Å
111213212223313233
T0.334700068854 Å20.0295106027539 Å2-0.00539076165494 Å2-0.317105983881 Å20.0728421959844 Å2--0.431168852565 Å2
L1.17979700566 °20.0457925623514 °20.00319670320526 °2-0.885443061006 °20.0613974479458 °2--2.02998818624 °2
S-0.0740961480635 Å °-0.166391012469 Å °0.0373208100883 Å °-0.109984896256 Å °-0.004327369617 Å °-0.238269884974 Å °-0.0991640698083 Å °0.151120568382 Å °0.0697004215107 Å °
Refinement TLS groupSelection details: all

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