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- PDB-5vsj: Sco GlgEI-V279S in complex with a pyrolidene-based ethyl-phosphon... -

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Basic information

Entry
Database: PDB / ID: 5vsj
TitleSco GlgEI-V279S in complex with a pyrolidene-based ethyl-phosphonate compound
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsTRANSFERASE / Streptomyces coelicolor / Maltosyltransferase / transition state analogue / Alpha-1 / 4-glucan
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / oligosaccharide catabolic process / hexosyltransferase activity / alpha-amylase activity
Similarity search - Function
: / GLGE, C-terminal / 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 / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...: / GLGE, C-terminal / 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 / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-9HV / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.456 Å
AuthorsPetit, C. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105084 United States
Citation
Journal: Org. Biomol. Chem. / Year: 2017
Title: Zwitterionic pyrrolidene-phosphonates: inhibitors of the glycoside hydrolase-like phosphorylase Streptomyces coelicolor GlgEI-V279S.
Authors: Veleti, S.K. / Petit, C. / Ronning, D.R. / Sucheck, S.J.
#1: Journal: Org. Biomol. Chem. / Year: 2017
Title: Zwitterionic pyrrolidene-phosphonates: inhibitors of the glycoside hydrolase-like phosphorylase Streptomyces coelicolor GlgEI-V279S.
Authors: Veleti, S.K. / Petit, C. / Ronning, D.R. / Sucheck, S.J.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)149,3475
Polymers148,3582
Non-polymers9893
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, homodimer in one asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-13 kcal/mol
Surface area51970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.855, 113.855, 317.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 74179.133 Da / Num. of mol.: 2 / Mutation: V279S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: glgE1, pep1, pep1A, pep1I, SCO5443, SC6A11.19c / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9L1K2, starch synthase (maltosyl-transferring)
#2: Chemical ChemComp-9HV / {2-[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]ethyl}phosphonic acid


Mass: 433.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28NO12P
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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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: 3.47 Å3/Da / Density % sol: 64.51 % / Description: Diamond
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium citrate pH 7.0 and 10 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→45.878 Å / Num. obs: 76413 / % possible obs: 99.1 % / Redundancy: 12.7 % / Net I/σ(I): 14.84
Reflection shellRedundancy: 13.3 % / Num. unique obs: 7224 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CN1

4cn1


Resolution: 2.456→45.878 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1999 2.62 %
Rwork0.2023 --
obs0.2033 76413 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.456→45.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10276 0 64 359 10699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310669
X-RAY DIFFRACTIONf_angle_d0.68114598
X-RAY DIFFRACTIONf_dihedral_angle_d2.3618724
X-RAY DIFFRACTIONf_chiral_restr0.0451589
X-RAY DIFFRACTIONf_plane_restr0.0051921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4558-2.51720.31451330.25274930X-RAY DIFFRACTION93
2.5172-2.58520.30441410.24975256X-RAY DIFFRACTION100
2.5852-2.66130.29211420.2315265X-RAY DIFFRACTION100
2.6613-2.74720.29321410.24225277X-RAY DIFFRACTION100
2.7472-2.84540.32711430.23725314X-RAY DIFFRACTION100
2.8454-2.95930.30111420.24155277X-RAY DIFFRACTION100
2.9593-3.09390.26371420.24355328X-RAY DIFFRACTION100
3.0939-3.2570.29591440.23785317X-RAY DIFFRACTION100
3.257-3.4610.28141430.22755315X-RAY DIFFRACTION100
3.461-3.72810.26321440.2165368X-RAY DIFFRACTION100
3.7281-4.10310.22571440.18465365X-RAY DIFFRACTION100
4.1031-4.69630.18941430.16185339X-RAY DIFFRACTION99
4.6963-5.91480.18231450.17045418X-RAY DIFFRACTION99
5.9148-45.88610.18971520.18095645X-RAY DIFFRACTION98

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