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- PDB-7mgy: Sco GlgEI-V279S in complex with 4-alpha-glucoside of valienamine -

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Basic information

Entry
Database: PDB / ID: 7mgy
TitleSco GlgEI-V279S in complex with 4-alpha-glucoside of valienamine
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsTRANSFERASE / CAZy glycoside hydrolase (GH)-like phosphorylase GH13_3 family / elongation of cytosolic glucan chains / maltosyl transferase
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / alpha-amylase activity / oligosaccharide catabolic process
Similarity search - Function
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / : / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / GLGE, C-terminal / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-ZD1 / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsJayasinghe, T.D. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI105084 United States
CitationJournal: Sci Rep / Year: 2021
Title: Stereoselective synthesis of a 4-⍺-glucoside of valienamine and its X-ray structure in complex with Streptomyces coelicolor GlgE1-V279S.
Authors: Si, A. / Jayasinghe, T.D. / Thanvi, R. / Ronning, D.R. / Sucheck, S.J.
History
DepositionApr 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.title / _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-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
B: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,1719
Polymers152,7892
Non-polymers1,3817
Water25,2931404
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint4 kcal/mol
Surface area50350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.784, 112.784, 310.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1 / GMPMT 1 / (1->4)-alpha-D-glucan:maltose-1-phosphate alpha-D-maltosyltransferase 1


Mass: 76394.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: glgE1, pep1, pep1A, pep1I, SCO5443, SC6A11.19c / Production host: Escherichia coli (E. coli)
References: UniProt: Q9L1K2, starch synthase (maltosyl-transferring)
#2: Chemical ChemComp-ZD1 / (1R,4S,5S,6R)-4-amino-5,6-dihydroxy-2-(hydroxymethyl)cyclohex-2-en-1-yl alpha-D-glucopyranoside


Mass: 337.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H23NO9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1404 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 mM Sodium citrate pH 7 and 10 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.83→55.48 Å / Num. obs: 176156 / % possible obs: 93.14 % / Redundancy: 16.3 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1802 / Rpim(I) all: 0.04559 / Rrim(I) all: 0.186 / Net I/σ(I): 9.28
Reflection shellResolution: 1.83→1.896 Å / Rmerge(I) obs: 6.231 / Mean I/σ(I) obs: 0.21 / Num. unique obs: 17390 / CC1/2: 0.436 / Rrim(I) all: 6.499

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U31

4u31


Resolution: 1.83→55.48 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 1867 1.14 %
Rwork0.1852 162217 -
obs0.1855 164084 93.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.83 Å2 / Biso mean: 33.6943 Å2 / Biso min: 17.66 Å2
Refinement stepCycle: final / Resolution: 1.83→55.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10211 0 93 1404 11708
Biso mean--38.93 39.82 -
Num. residues----1298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.880.7028340.71422319235318
1.88-1.940.39211380.3676121911232993
1.94-20.33591520.28911324513397100
2-2.070.28361520.23951324213394100
2.07-2.150.25831520.22291325413406100
2.15-2.250.27451530.22151331213465100
2.25-2.370.23011520.20211328713439100
2.37-2.520.22421540.1931334713501100
2.52-2.710.22741530.1951333813491100
2.71-2.980.25611540.19711343313587100
2.98-3.420.23331550.18131349313648100
3.42-4.30.16361570.14831361613773100
4.3-55.480.1581610.1451414014301100

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