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- PDB-7uvd: Sco GlgEI-V279S in complex with cyclohexyl carbasugar -

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Basic information

Entry
Database: PDB / ID: 7uvd
TitleSco GlgEI-V279S in complex with cyclohexyl carbasugar
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsTRANSFERASE / M1P binding site / cyclohexyl carbasugar
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 / 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.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: To Be Published
Title: Sco GlgEI-V279S in complex with cyclohexyl carbasugar
Authors: Jayasinghe, T.D. / Ronning, D.R.
History
DepositionApr 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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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)153,8406
Polymers152,7892
Non-polymers1,0514
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-11 kcal/mol
Surface area51070 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 / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 289.5 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: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 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: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 1800 3.47 %
Rwork0.1904 50108 -
obs0.1928 51908 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.82 Å2 / Biso mean: 57.7764 Å2 / Biso min: 26.01 Å2
Refinement stepCycle: final / Resolution: 2.73→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10276 0 72 250 10598
Biso mean--69.8 52.06 -
Num. residues----1297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910734
X-RAY DIFFRACTIONf_angle_d1.15314682
X-RAY DIFFRACTIONf_dihedral_angle_d7.9411494
X-RAY DIFFRACTIONf_chiral_restr0.0611594
X-RAY DIFFRACTIONf_plane_restr0.0131936
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3914X-RAY DIFFRACTION1.473TORSIONAL
12B3914X-RAY DIFFRACTION1.473TORSIONAL
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 (%)
2.73-2.80.38321400.312439104050100
2.8-2.890.37591420.280739364078100
2.89-2.980.33821400.266939124052100
2.98-3.090.32741420.24539234065100
3.09-3.210.35361420.239639654107100
3.21-3.360.28161410.226139344075100
3.36-3.530.31251420.227439574099100
3.53-3.750.30341430.20253958410199
3.75-4.040.28581400.17323923406399
4.04-4.450.21831340.15313703383792
4.45-5.090.17941260.14283509363587
5.09-6.410.20981330.16083700383391
6.42-49.40.20561350.16263778391387

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