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

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Basic information

Entry
Database: PDB / ID: 5cim
TitleStructure of Mycobacterium thermoresistibile GlgE in complex with maltose (cocrystallisation with maltose-1-phosphate) at 3.32A 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 / 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 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / 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 / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 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 13, 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 / 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.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
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)155,5793
Polymers155,2362
Non-polymers3421
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-10 kcal/mol
Surface area49680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.537, 112.967, 221.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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.: 1
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG300, citrate-phosphate buffer pH4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.318→221.433 Å / Num. all: 29571 / Num. obs: 29571 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 81.93 Å2 / Rpim(I) all: 0.045 / Rrim(I) all: 0.103 / Rsym value: 0.083 / Net I/av σ(I): 8.917 / Net I/σ(I): 16 / Num. measured all: 149129
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.318-3.55.20.5971.32217942560.3180.5973.199.8
3.5-3.715.10.3562.12055840390.1920.356599.9
3.71-3.975.10.2443.11909937750.1330.244799.9
3.97-4.285.20.1335.81830635470.0720.13311.499.8
4.28-4.6950.0829.31633732580.0450.08216.799.9
4.69-5.255.10.06411.81525229720.0340.06420.699.9
5.25-6.0650.05813.11326226370.0320.05821.999.8
6.06-7.424.90.04416.31108322550.0240.04427.499.8
7.42-10.494.80.02227.6851417850.0120.02245.999.4
10.49-221.4334.30.01830.2453910470.0110.01852.498.7

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.0refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CGM

5cgm


Resolution: 3.32→100.63 Å / Cor.coef. Fo:Fc: 0.9321 / Cor.coef. Fo:Fc free: 0.9152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.409
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1494 5.07 %RANDOM
Rwork0.1783 ---
obs0.1801 29449 99.69 %-
Displacement parametersBiso max: 214.01 Å2 / Biso mean: 110.42 Å2 / Biso min: 42.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.4684 Å20 Å20 Å2
2---21.5357 Å20 Å2
3---20.0674 Å2
Refine analyzeLuzzati coordinate error obs: 0.715 Å
Refinement stepCycle: final / Resolution: 3.32→100.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10135 0 45 66 10246
Biso mean--120.59 70.75 -
Num. residues----1311
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3317SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes222HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1560HARMONIC5
X-RAY DIFFRACTIONt_it10490HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1328SEMIHARMONIC5
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_contact12082SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10490HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14390HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion21.26
LS refinement shellResolution: 3.32→3.44 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2688 136 4.79 %
Rwork0.2151 2701 -
all0.2176 2837 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4791-0.21260.28881.6034-0.32692.8964-0.01960.1239-0.0827-0.2199-0.12410.16010.06320.17110.1437-0.07680.0407-0.0541-0.0533-0.0581-0.3203-12.6245-16.32429.7895
20.94980.13761.20380.3234-0.47283.3724-0.0966-0.0665-0.04180.43270.08330.3068-0.6747-0.85190.01330.30360.26670.18530.121-0.0186-0.3778-34.6827-9.577665.9358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 696
2X-RAY DIFFRACTION2{ B|* }B0 - 696

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