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- PDB-8im8: Crystal structure of Periplasmic alpha-amylase (MalS) from E.coli -

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Basic information

Entry
Database: PDB / ID: 8im8
TitleCrystal structure of Periplasmic alpha-amylase (MalS) from E.coli
ComponentsPeriplasmic alpha-amylase
KeywordsHYDROLASE / maltooligosaccharides / malS / GH13 / Glycosidase / STRUCTURAL PROTEIN
Function / homology
Function and homology information


alpha-glucan catabolic process / alpha-amylase / alpha-amylase activity / outer membrane-bounded periplasmic space / periplasmic space / calcium ion binding
Similarity search - Function
Alpha-amylase, MalS type / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Periplasmic alpha-amylase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAn, Y. / Park, J.T. / Park, K.H. / Woo, E.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2023
Title: The Distinctive Permutated Domain Structure of Periplasmic alpha-Amylase (MalS) from Glycoside Hydrolase Family 13 Subfamily 19.
Authors: An, Y. / Tran, P.L. / Yoo, M.J. / Song, H.N. / Park, K.H. / Kim, T.J. / Park, J.T. / Woo, E.J.
History
DepositionMar 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic alpha-amylase
B: Periplasmic alpha-amylase
C: Periplasmic alpha-amylase
D: Periplasmic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,48212
Polymers303,1614
Non-polymers3218
Water5,260292
1
A: Periplasmic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8713
Polymers75,7901
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21790 Å2
MethodPISA
2
B: Periplasmic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8713
Polymers75,7901
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21520 Å2
MethodPISA
3
C: Periplasmic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8713
Polymers75,7901
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area21710 Å2
MethodPISA
4
D: Periplasmic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8713
Polymers75,7901
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.242, 133.242, 386.269
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11D-870-

HOH

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Components

#1: Protein
Periplasmic alpha-amylase / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 75790.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: malS, b3571, JW3543 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25718, alpha-amylase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium citrate tribasic dihydrate pH5.5 20% w/v Polyehtylene glycol 1000 0.1M Lthium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 30, 2015 / Details: 1EA9, 5A2A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20.02 Å / Num. obs: 69932 / % possible obs: 99.83 % / Redundancy: 11.4 % / Biso Wilson estimate: 44.25 Å2 / Rrim(I) all: 0.123 / Net I/σ(I): 168
Reflection shellResolution: 2.7→2.77 Å / Mean I/σ(I) obs: 5.5 / Num. unique obs: 4802 / Rrim(I) all: 0.684 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA9, 5A2A

1ea9

5a2a


Resolution: 2.7→20.02 Å / SU ML: 0.3187 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.7265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 2023 2.89 %
Rwork0.178 67909 -
obs0.1796 69932 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.44 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17748 0 8 292 18048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010118268
X-RAY DIFFRACTIONf_angle_d1.210624828
X-RAY DIFFRACTIONf_chiral_restr0.06472520
X-RAY DIFFRACTIONf_plane_restr0.00933248
X-RAY DIFFRACTIONf_dihedral_angle_d12.04686436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.33591450.24244802X-RAY DIFFRACTION98.53
2.77-2.840.32681400.23294857X-RAY DIFFRACTION99.94
2.84-2.930.32151470.23234813X-RAY DIFFRACTION99.92
2.93-3.020.28141450.21924882X-RAY DIFFRACTION99.94
3.02-3.130.31471480.24044883X-RAY DIFFRACTION99.96
3.13-3.250.28211450.20894869X-RAY DIFFRACTION99.96
3.25-3.40.30691400.21644856X-RAY DIFFRACTION99.98
3.4-3.580.24471470.18344803X-RAY DIFFRACTION99.96
3.58-3.80.24351400.17324848X-RAY DIFFRACTION99.98
3.8-4.090.2281430.1644859X-RAY DIFFRACTION99.82
4.09-4.50.2171460.14924880X-RAY DIFFRACTION100
4.5-5.140.15211420.14034864X-RAY DIFFRACTION99.96
5.14-6.440.19511460.16034841X-RAY DIFFRACTION99.98
6.44-20.020.17661490.14854852X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: -13.3721715185 Å / Origin y: 42.4147738286 Å / Origin z: 340.955066158 Å
111213212223313233
T0.287857734054 Å2-0.0290278059085 Å2-0.00402392934338 Å2-0.273203642281 Å20.0487748579814 Å2--0.305772654643 Å2
L0.0726080796553 °2-0.0381408949528 °20.112651946087 °2-0.142931102367 °2-0.147623329537 °2--0.445013534579 °2
S0.00477995040096 Å °-0.0266010097729 Å °-0.0762013489968 Å °2.13657181141E-5 Å °0.02470233459 Å °0.0766227660225 Å °0.125286068481 Å °-0.0403074265182 Å °-0.0202306001175 Å °
Refinement TLS groupSelection details: all

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