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- PDB-4u31: Sco GlgEI-V279S in Complex with maltose-C-phosphonate -

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Basic information

Entry
Database: PDB / ID: 4u31
TitleSco GlgEI-V279S in Complex with maltose-C-phosphonate
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsTRANSFERASE / Inhibitors Complex Maltose-C-phosphonate 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
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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...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 / 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
alpha-maltose-c-phosphonate / CITRIC ACID / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.849 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: Sci Rep / Year: 2015
Title: Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors.
Authors: Lindenberger, J.J. / Kumar Veleti, S. / Wilson, B.N. / Sucheck, S.J. / Ronning, D.R.
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 / Non-polymer description
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 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_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _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 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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

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)154,32411
Polymers152,7892
Non-polymers1,5359
Water26,0681447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint3 kcal/mol
Surface area50980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.556, 113.556, 315.142
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)-(1S)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol / alpha-maltose-c-phosphonate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 420.304 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose-c-phosphonate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[h12122h_2-6_1*PO/2O/2=O][a2122h-1a_1-5]/1-2/a5-b1WURCSPDB2Glycan 1.1.0
[][<C7O7P1>]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1447 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
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: 1.8→50 Å / Num. obs: 175910 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 21.66 Å2 / Net I/σ(I): 37.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementResolution: 1.849→42.685 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 2000 1.14 %
Rwork0.1643 173910 -
obs0.1646 175910 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.67 Å2 / Biso mean: 24.4864 Å2 / Biso min: 9.93 Å2
Refinement stepCycle: final / Resolution: 1.849→42.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10276 0 100 1447 11823
Biso mean--22.99 31.82 -
Num. residues----1297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110767
X-RAY DIFFRACTIONf_angle_d1.34914730
X-RAY DIFFRACTIONf_chiral_restr0.0461595
X-RAY DIFFRACTIONf_plane_restr0.0091946
X-RAY DIFFRACTIONf_dihedral_angle_d13.593933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.849-1.89520.22421410.19881226412405
1.8952-1.94650.20881400.18961221312353
1.9465-2.00370.21341410.18221230012441
2.0037-2.06840.22211430.1811231012453
2.0684-2.14230.21771410.17211231512456
2.1423-2.22810.21681420.17311230412446
2.2281-2.32950.20471410.17141231112452
2.3295-2.45230.20711420.17381232112463
2.4523-2.60590.20411420.17371238912531
2.6059-2.80710.20561420.17571242812570
2.8071-3.08950.19051430.17921246612609
3.0895-3.53640.21011450.17111252612671
3.5364-4.45470.15471460.14021265312799
4.4547-42.6960.1781510.13881311013261

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