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- PDB-7mel: Sco GlgEI-V279S in complex with 4-alpha-glucoside of validamine -

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Basic information

Entry
Database: PDB / ID: 7mel
TitleSco GlgEI-V279S in complex with 4-alpha-glucoside of validamine
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 / oligosaccharide catabolic process / alpha-amylase activity
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-Z3D / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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-alpha-glucoside of valienamine and its X-ray structure in complex with Streptomyces coelicolor GlgE1-V279S.
Authors: Si, A. / Jayasinghe, T.D. / Thanvi, R. / Kapil, S. / Ronning, D.R. / Sucheck, S.J.
History
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)154,15711
Polymers152,7892
Non-polymers1,3689
Water28,8601602
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-21 kcal/mol
Surface area51360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.049, 113.049, 311.506
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 6 types, 1611 molecules

#2: Chemical ChemComp-Z3D / (1R,2R,3S,4S,6R)-4-amino-2,3-dihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside


Mass: 339.339 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H25NO9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1602 / 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: 3.19 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 mM Sodium citrate pH 7 and 10 % PEG 3,350

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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: 1.75→55.78 Å / Num. obs: 195923 / % possible obs: 96.21 % / Redundancy: 11.6 % / Biso Wilson estimate: 23.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09187 / Rpim(I) all: 0.02625 / Rrim(I) all: 0.09576 / Net I/σ(I): 16.2
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.308 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 14983 / CC1/2: 0.357 / CC star: 0.725 / Rpim(I) all: 0.9307 / Rrim(I) all: 1.618 / % possible all: 71.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u31

4u31


Resolution: 1.75→55.78 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 3734 1.02 %
Rwork0.1762 362436 -
obs0.1764 195923 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.13 Å2 / Biso mean: 26.4027 Å2 / Biso min: 13.05 Å2
Refinement stepCycle: final / Resolution: 1.75→55.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10238 0 88 1602 11928
Biso mean--29.96 33.83 -
Num. residues----1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810660
X-RAY DIFFRACTIONf_angle_d0.88914573
X-RAY DIFFRACTIONf_chiral_restr0.0571589
X-RAY DIFFRACTIONf_plane_restr0.011916
X-RAY DIFFRACTIONf_dihedral_angle_d8.7911475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.4437650.4576401646645
1.77-1.790.4065800.40318413849359
1.79-1.820.39621060.3385101541026071
1.82-1.850.33421230.3074117161183982
1.85-1.870.30261320.2732127671289990
1.87-1.90.28561410.2479135451368695
1.9-1.930.20931470.2362139711411898
1.93-1.970.27761440.22091424314387100
1.97-20.28641460.21571427114417100
2-2.040.24941480.21141421914367100
2.04-2.080.22051450.20661430914454100
2.08-2.130.27051490.17911432314472100
2.13-2.180.16841480.17281428014428100
2.18-2.230.17641470.17331422114368100
2.23-2.290.21151500.16971427614426100
2.29-2.360.2151460.17151432914475100
2.36-2.440.22251440.17361424314387100
2.44-2.520.17091520.17651428114433100
2.52-2.620.26621470.18231427714424100
2.62-2.740.20821460.18511426514411100
2.74-2.890.1791450.17861428514430100
2.89-3.070.24131450.18551427314418100
3.07-3.310.20291470.17551427814425100
3.31-3.640.16831470.15761430414451100
3.64-4.160.12711490.14231425614405100
4.16-5.250.14621450.12391426914414100
5.25-55.780.16021500.15271426714417100

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