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- PDB-5cgm: Structure of Mycobacterium thermoresistibile GlgE in complex with... -

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Basic information

Entry
Database: PDB / ID: 5cgm
TitleStructure of Mycobacterium thermoresistibile GlgE in complex with maltose at 1.95A resolution
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
KeywordsTRANSFERASE / GlgE / Maltose / GH13 / maltosyltransferase
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds
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 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...: / 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 / Alpha amylase, catalytic domain / 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMendes, V. / Blaszczyk, M. / Maranha, A. / Empadinhas, N. / Blundell, T.L.
CitationJournal: Sci Rep / Year: 2015
Title: Structure of Mycobacterium thermoresistibile GlgE defines novel conformational states that contribute to the catalytic mechanism.
Authors: Mendes, V. / Blaszczyk, M. / Maranha, A. / Empadinhas, N. / Blundell, T.L.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
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 / diffrn_radiation_wavelength / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.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.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...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
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
B: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,27551
Polymers155,2362
Non-polymers4,03949
Water16,826934
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14770 Å2
ΔGint-203 kcal/mol
Surface area49530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.330, 113.900, 220.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / GMPMT / (1->4)-alpha-D-glucan:maltose-1-phosphate alpha-D-maltosyltransferase


Mass: 77618.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile ATCC 19527 (bacteria)
Gene: glgE, KEK_12948 / Production host: Escherichia coli (E. coli)
References: UniProt: G7CL00, starch synthase (maltosyl-transferring)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 9 types, 981 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 934 / 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: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 300, sodium phosphate-citrate, maltose / PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.95→37.74 Å / Num. obs: 147668 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.187 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.95-1.9813.71.8332.29951172410.8470.51299.9
10.68-37.74130.04735.81328010240.9990.01498

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
Aimless0.1.26data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZSS

3zss


Resolution: 1.95→19.66 Å / Cor.coef. Fo:Fc: 0.9269 / Cor.coef. Fo:Fc free: 0.9089 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 7386 5.01 %RANDOM
Rwork0.1754 ---
obs0.1768 147417 99.87 %-
Displacement parametersBiso mean: 32.91 Å2
Baniso -1Baniso -2Baniso -3
1--13.2663 Å20 Å20 Å2
2--2.1587 Å20 Å2
3---11.1076 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10415 0 1228 934 12577
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110995HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9915040HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3529SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes229HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1622HARMONIC5
X-RAY DIFFRACTIONt_it10995HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion14.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1376SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12604SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2419 564 5.23 %
Rwork0.2163 10227 -
all0.2176 10791 -
obs--99.87 %

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