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- PDB-6m4k: X-ray crystal structure of wild type alpha-amylase I from Eisenia... -

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Basic information

Entry
Database: PDB / ID: 6m4k
TitleX-ray crystal structure of wild type alpha-amylase I from Eisenia fetida
ComponentsAlpha-amylase
KeywordsHYDROLASE / TIM barrel / GH family 13 / carbohydrase / cold-active
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / Alpha-amylase
Similarity search - Component
Biological speciesEisenia fetida (common brandling worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHirano, Y. / Tsukamoto, K. / Ariki, S. / Naka, Y. / Ueda, M. / Tamada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: X-ray crystallographic structural studies of alpha-amylase I from Eisenia fetida.
Authors: Hirano, Y. / Tsukamoto, K. / Ariki, S. / Naka, Y. / Ueda, M. / Tamada, T.
History
DepositionMar 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)59,59212
Polymers58,3501
Non-polymers1,24211
Water13,205733
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.245, 96.245, 121.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-610-

PG4

21A-894-

HOH

31A-899-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-amylase /


Mass: 58349.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eisenia fetida (common brandling worm) / Gene: alpha-amylase / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A173N065, alpha-amylase

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Non-polymers , 7 types, 744 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.3 M lithium sulfate, 3% (v/v) PEG 400, 0.1 M magnesium chloride, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 11, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→49.2203 Å / Num. obs: 160191 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 16.5515777525 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.056 / Net I/σ(I): 20.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 7805 / CC1/2: 0.847 / Rrim(I) all: 0.965 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KXQ

1kxq


Resolution: 1.3→49.22 Å / SU ML: 0.112884114388 / Cross valid method: FREE R-VALUE / σ(F): 1.33016062502 / Phase error: 18.9317217916
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183266623059 8087 5.05090250453 %
Rwork0.167132596014 152023 -
obs0.167933873213 160110 99.9825150807 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.1494242133 Å2
Refinement stepCycle: LAST / Resolution: 1.3→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 73 733 4715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005450620504894728
X-RAY DIFFRACTIONf_angle_d0.8562660458776469
X-RAY DIFFRACTIONf_chiral_restr0.0821277962344636
X-RAY DIFFRACTIONf_plane_restr0.00624410812954883
X-RAY DIFFRACTIONf_dihedral_angle_d13.67290283661712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.2691335622642650.2625743908664977X-RAY DIFFRACTION99.9809269502
1.3148-1.33020.2517964574212740.2514493806834993X-RAY DIFFRACTION100
1.3302-1.34650.2705989713792460.2465120264445053X-RAY DIFFRACTION100
1.3465-1.36350.2455350095182830.2385720926145027X-RAY DIFFRACTION100
1.3635-1.38150.2429930834262240.225850919145065X-RAY DIFFRACTION99.9810964083
1.3815-1.40040.2179578063792760.2226747415995020X-RAY DIFFRACTION99.9622499056
1.4004-1.42040.2313508775822600.2197499830865027X-RAY DIFFRACTION99.9810892587
1.4204-1.44160.2313688786642440.2160366644055062X-RAY DIFFRACTION100
1.4416-1.46410.2265491754183020.212823487624991X-RAY DIFFRACTION99.9811106913
1.4641-1.48810.2155590095532850.2015879640395037X-RAY DIFFRACTION99.9812136014
1.4881-1.51380.2089855385333220.1946621252644954X-RAY DIFFRACTION100
1.5138-1.54130.2023831197692920.1944200247555034X-RAY DIFFRACTION100
1.5413-1.5710.2302270259672750.1926982940665056X-RAY DIFFRACTION100
1.571-1.6030.2188785345642590.1889095806865056X-RAY DIFFRACTION100
1.603-1.63790.2038281819172710.1857496120764995X-RAY DIFFRACTION100
1.6379-1.6760.2095184175512830.1835015326835023X-RAY DIFFRACTION99.9811569625
1.676-1.71790.1978905619842830.1839447287195067X-RAY DIFFRACTION99.9813119043
1.7179-1.76440.1931523796712390.1833813718615059X-RAY DIFFRACTION99.9811285148
1.7644-1.81630.2085042075462890.1791023226485041X-RAY DIFFRACTION99.9812417933
1.8163-1.87490.2092742649362830.1762336448925053X-RAY DIFFRACTION99.9812628818
1.8749-1.94190.182137105062680.1651990591785080X-RAY DIFFRACTION100
1.9419-2.01970.1704021811922680.1655453539225065X-RAY DIFFRACTION100
2.0197-2.11160.1883674710832500.16317586615085X-RAY DIFFRACTION100
2.1116-2.22290.1635614640542520.1537251759625125X-RAY DIFFRACTION99.9628183677
2.2229-2.36220.1677954783242600.1545140386595072X-RAY DIFFRACTION99.9812488281
2.3622-2.54460.1653769935832260.1611091505515184X-RAY DIFFRACTION100
2.5446-2.80060.185615269642730.1657668147945099X-RAY DIFFRACTION99.9441860465
2.8006-3.20580.1813160500972890.1620093588745155X-RAY DIFFRACTION100
3.2058-4.03870.1485361283622780.1380916978255179X-RAY DIFFRACTION99.9816782704
4.0387-49.220.1750891430672680.1568250829935389X-RAY DIFFRACTION99.8411577833

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