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- PDB-5vt4: Sco GlgEI-V279S in complex with a pyrolidene-based methyl-phospho... -

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Basic information

Entry
Database: PDB / ID: 5vt4
TitleSco GlgEI-V279S in complex with a pyrolidene-based methyl-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 / 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 / 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 ...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 / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-9KJ / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.205 Å
AuthorsPetit, C. / Ronning, D.R. / Lindenberger, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105084 United States
CitationJournal: 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 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / 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 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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
C: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
D: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,3948
Polymers296,7174
Non-polymers1,6774
Water1,04558
1
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)149,1974
Polymers148,3582
Non-polymers8392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-17 kcal/mol
Surface area50950 Å2
MethodPISA
2
C: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
D: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1974
Polymers148,3582
Non-polymers8392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-19 kcal/mol
Surface area50810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.851, 113.851, 312.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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.: 4 / 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 / Plasmid: pET32 / Cell (production host): BL21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9L1K2, starch synthase (maltosyl-transferring)
#2: Sugar
ChemComp-9KJ / {[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid / {[(2R,3R,4R,5R)-3-(alpha-D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid / {[(2R,3R,4R,5R)-3-(D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid / {[(2R,3R,4R,5R)-3-(glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid


Type: D-saccharide / Mass: 419.319 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H26NO12P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.42 Å3/Da / Density % sol: 64 % / Description: Diamond
Crystal growTemperature: 293.16 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 300 mm CCD / Detector: CCD / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.2→39.061 Å / Num. obs: 64431 / % possible obs: 99.6 % / Redundancy: 4.3 % / Net I/σ(I): 11.5
Reflection shellHighest resolution: 3.2 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXmodel building
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cn1

4cn1


Resolution: 3.205→39.061 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2394 1998 3.1 %
Rwork0.2069 --
obs0.2079 64431 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.205→39.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20292 0 108 58 20458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521006
X-RAY DIFFRACTIONf_angle_d1.03928761
X-RAY DIFFRACTIONf_dihedral_angle_d11.9627590
X-RAY DIFFRACTIONf_chiral_restr0.0443153
X-RAY DIFFRACTIONf_plane_restr0.0063780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2049-3.2850.30721410.28094353X-RAY DIFFRACTION96
3.285-3.37380.35041420.27024444X-RAY DIFFRACTION100
3.3738-3.4730.3031480.26154478X-RAY DIFFRACTION100
3.473-3.5850.28771460.24694493X-RAY DIFFRACTION100
3.585-3.7130.27851400.24084432X-RAY DIFFRACTION100
3.713-3.86160.29481440.24124466X-RAY DIFFRACTION100
3.8616-4.03710.23161400.22344483X-RAY DIFFRACTION99
4.0371-4.24970.24331390.21444499X-RAY DIFFRACTION100
4.2497-4.51560.22121420.19844449X-RAY DIFFRACTION100
4.5156-4.86370.21831420.19194480X-RAY DIFFRACTION100
4.8637-5.35210.2221440.1864489X-RAY DIFFRACTION100
5.3521-6.12390.21971450.20414457X-RAY DIFFRACTION99
6.1239-7.70580.22551430.19354495X-RAY DIFFRACTION100
7.7058-39.06410.18961420.15164415X-RAY DIFFRACTION97

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