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- PDB-4u2z: X-ray crystal structure of an Sco GlgEI-V279S/1,2,2-trifluromalto... -

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Basic information

Entry
Database: PDB / ID: 4u2z
TitleX-ray crystal structure of an Sco GlgEI-V279S/1,2,2-trifluromaltose complex
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsTRANSFERASE / Inhibitor Complex Fluorosugar 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
: / 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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...: / 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 / Golgi alpha-mannosidase II / 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
1,2,2-trifluoromaltose / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRonning, 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: 2015
Title: Synthesis of 2-deoxy-2,2-difluoro-alpha-maltosyl fluoride and its X-ray structure in complex with Streptomyces coelicolor GlgEI-V279S.
Authors: Thanna, S. / Lindenberger, J.J. / Gaitonde, V.V. / Ronning, D.R. / Sucheck, S.J.
History
DepositionJul 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)153,5184
Polymers152,7892
Non-polymers7292
Water16,051891
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-16 kcal/mol
Surface area51560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.297, 113.297, 314.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 76394.547 Da / Num. of mol.: 2 / Mutation: V279S
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)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-2-deoxy-2,2-difluoro-alpha-D-arabino-hexopyranosyl fluoride / 1 / 2 / 2-trifluoromaltose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 364.269 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 1,2,2-trifluoromaltose
DescriptorTypeProgram
[][a-D-Manp1fluoro2fluoro]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / 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: 64.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium citrate pH 7.0 and 10 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.08 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 96584 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 33.7 Å2 / Net I/σ(I): 26

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Processing

Software
NameVersionClassification
HKL-3000phasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→42.584 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 4826 5 %
Rwork0.1629 91654 -
obs0.1647 96480 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.58 Å2 / Biso mean: 35.9062 Å2 / Biso min: 18.49 Å2
Refinement stepCycle: final / Resolution: 2.26→42.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10276 0 48 891 11215
Biso mean--36.93 38.33 -
Num. residues----1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810630
X-RAY DIFFRACTIONf_angle_d1.09414542
X-RAY DIFFRACTIONf_chiral_restr0.0431584
X-RAY DIFFRACTIONf_plane_restr0.0061914
X-RAY DIFFRACTIONf_dihedral_angle_d12.2233862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2601-2.28580.26771560.207729633119100
2.2858-2.31260.27921600.199330413201100
2.3126-2.34080.23781560.190529823138100
2.3408-2.37050.2321600.189230303190100
2.3705-2.40170.24741570.188130043161100
2.4017-2.43460.2521590.187530213180100
2.4346-2.46930.25461590.190330073166100
2.4693-2.50620.20871600.186430203180100
2.5062-2.54530.26611570.190329913148100
2.5453-2.58710.23991610.182630583219100
2.5871-2.63170.22341580.183230153173100
2.6317-2.67950.24381590.180730073166100
2.6795-2.73110.24981580.181330053163100
2.7311-2.78680.22991610.18330553216100
2.7868-2.84740.23541600.174230223182100
2.8474-2.91360.21691600.179730483208100
2.9136-2.98640.22731590.18330253184100
2.9864-3.06720.251610.179930503211100
3.0672-3.15740.20891600.189130323192100
3.1574-3.25930.21351600.186130383198100
3.2593-3.37570.22231610.178230543215100
3.3757-3.51080.191610.168630573218100
3.5108-3.67050.20671620.167730723234100
3.6705-3.86390.18251610.163830663227100
3.8639-4.10580.17121630.142230943257100
4.1058-4.42250.16351630.126630903253100
4.4225-4.8670.14671650.123131293294100
4.867-5.56990.16141640.133331293293100
5.5699-7.01250.17361680.151331993367100
7.0125-42.59120.15491770.14163350352799

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