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- PDB-8d6k: Sco GlgEI-V279S in complex with cyclohexyl carbasugar -

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Basic information

Entry
Database: PDB / ID: 8d6k
TitleSco GlgEI-V279S in complex with cyclohexyl carbasugar
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsTRANSFERASE / complex with GlgE
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 / Chem-RT6 / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsJayasinghe, T.J. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Chem / Year: 2022
Title: Synthesis of C 7 /C 8 -cyclitols and C 7 N-aminocyclitols from maltose and X-ray crystal structure of Streptomyces coelicolor GlgEI V279S in a complex with an amylostatin GXG-like derivative.
Authors: Thanvi, R. / Jayasinghe, T.D. / Kapil, S. / Obadawo, B.S. / Ronning, D.R. / Sucheck, S.J.
History
DepositionJun 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
A: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,7345
Polymers152,7892
Non-polymers9453
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-12 kcal/mol
Surface area51250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.438, 112.438, 310.411
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 15 through 24 or resid 26...
21(chain B and (resid 15 through 24 or resid 26...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU(chain A and (resid 15 through 24 or resid 26...AB15 - 2415 - 24
12VALVALVALVAL(chain A and (resid 15 through 24 or resid 26...AB2626
13PROPROALAALA(chain A and (resid 15 through 24 or resid 26...AB28 - 24428 - 244
14GLYGLYGLNGLN(chain A and (resid 15 through 24 or resid 26...AB246 - 324246 - 324
15SERSERALAALA(chain A and (resid 15 through 24 or resid 26...AB326 - 467326 - 467
16TYRTYRTHRTHR(chain A and (resid 15 through 24 or resid 26...AB469 - 557469 - 557
17LEULEUGLYGLY(chain A and (resid 15 through 24 or resid 26...AB559 - 652559 - 652
18THRTHRARGARG(chain A and (resid 15 through 24 or resid 26...AB654 - 663654 - 663
21PROPROLEULEU(chain B and (resid 15 through 24 or resid 26...BA15 - 2415 - 24
22VALVALVALVAL(chain B and (resid 15 through 24 or resid 26...BA2626
23PROPROALAALA(chain B and (resid 15 through 24 or resid 26...BA28 - 24428 - 244
24GLYGLYGLNGLN(chain B and (resid 15 through 24 or resid 26...BA246 - 324246 - 324
25SERSERSERSER(chain B and (resid 15 through 24 or resid 26...BA326326
26LEULEULEULEU(chain B and (resid 15 through 24 or resid 26...BA559559
27LEULEUGLYGLY(chain B and (resid 15 through 24 or resid 26...BA559 - 652559 - 652
28THRTHRARGARG(chain B and (resid 15 through 24 or resid 26...BA654 - 663654 - 663

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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 A3(2) (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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-RT6 / (1R,4S,5S,6R)-4-(cyclohexylamino)-5,6-dihydroxy-2-(hydroxymethyl)cyclohex-2-en-1-yl alpha-D-glucopyranoside


Mass: 419.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H33NO9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.2 M sodium citrate pH 7.0 and 10 % W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.73→49.4 Å / Num. obs: 51908 / % possible obs: 96.28 % / Redundancy: 7.5 % / CC1/2: 0.988 / Rpim(I) all: 0.112 / Net I/σ(I): 1.1
Reflection shellResolution: 2.73→2.828 Å / Num. unique obs: 5263 / CC1/2: 0.455

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U31

4u31


Resolution: 2.73→49.4 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1800 3.47 %
Rwork0.1909 50108 -
obs0.1932 51908 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.06 Å2 / Biso mean: 58.1058 Å2 / Biso min: 27.54 Å2
Refinement stepCycle: final / Resolution: 2.73→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10276 0 65 249 10590
Biso mean--72.12 52.28 -
Num. residues----1297
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3914X-RAY DIFFRACTION2.887TORSIONAL
12B3914X-RAY DIFFRACTION2.887TORSIONAL
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 (%)
2.73-2.80.37891400.311439104050100
2.8-2.890.37291420.282839364078100
2.89-2.980.33941400.270739124052100
2.98-3.090.33431420.248239234065100
3.09-3.210.35141420.240939654107100
3.21-3.360.2841410.227739344075100
3.36-3.530.31031420.226739574099100
3.53-3.750.30281430.20243958410199
3.75-4.040.27431400.17223923406399
4.04-4.450.22261340.15373703383792
4.45-5.090.18041260.14323509363587
5.09-6.410.21051330.16293700383391
6.42-49.40.20621350.16143778391387

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