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- PDB-5lgw: GlgE isoform 1 from Streptomyces coelicolor D394A mutant co-cryst... -

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Basic information

Entry
Database: PDB / ID: 5lgw
TitleGlgE isoform 1 from Streptomyces coelicolor D394A mutant co-crystallised with maltodextrin
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsHYDROLASE / alpha-glucan biosynthesis / glycoside hydrolase family 13_3 / transferase
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
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 domain / Glycosyl hydrolase, family 13, catalytic domain / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily ...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 domain / Glycosyl hydrolase, family 13, catalytic domain / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Immunoglobulin-like fold / Alpha-Beta Barrel / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta-maltose / alpha-maltopentaose / CITRIC ACID / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSyson, K. / Stevenson, C.E.M. / Mia, F. / Barclay, J.E. / Tang, M. / Gorelik, A. / Rashid, A.M. / Lawson, D.M. / Bornemann, S.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I012850/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilDoctoral Training Partnership United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Ligand-bound structures and site-directed mutagenesis identify the acceptor and secondary binding sites of Streptomyces coelicolor maltosyltransferase GlgE.
Authors: Syson, K. / Stevenson, C.E. / Miah, F. / Barclay, J.E. / Tang, M. / Gorelik, A. / Rashid, A.M. / Lawson, D.M. / Bornemann, S.
History
DepositionJul 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: 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 / pdbx_struct_assembly_gen / 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.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 / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)160,29213
Polymers155,0422
Non-polymers5,25111
Water19,6721092
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12670 Å2
ΔGint66 kcal/mol
Surface area51130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.110, 115.110, 311.360
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
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 662
2010B15 - 662

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Components

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Protein , 1 types, 2 molecules AB

#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: 77520.836 Da / Num. of mol.: 2 / Mutation: D394A
Source method: isolated from a genetically manipulated source
Details: D394A variant expressed with a twenty residue nickel affinity tag with sequence MGSSHHHHHHSSGLVPRGSH appended to the N-terminus of the full-length amino acid sequence being derived from the pET-15b vector
Source: (gene. exp.) Streptomyces coelicolor (unknown) / Gene: glgE1, pep1, pep1A, pep1I, SCO5443, SC6A11.19c / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (unknown) / Variant (production host): pLysS
References: UniProt: Q9L1K2, starch synthase (maltosyl-transferring)

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Sugars , 4 types, 6 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1477.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-6[DGlcpa1-4DGlcpa1-4]DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,9,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1-1/a4-b1_b4-c1_b6-e1_c4-d1_e4-f1_f4-g1_g4-h1_h4-i1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}[(6+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a6-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-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: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 1097 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1092 / 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: 3.33 Å3/Da / Density % sol: 63.02 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→81.4 Å / Num. obs: 147828 / % possible obs: 97.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 26.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/av σ(I): 17.5 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.95-23.10.9151.20.589179.9
8.72-81.415.60.0360.999199.4

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZST
Resolution: 1.95→81.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.806 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1507 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.113
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 7409 5 %RANDOM
Rwork0.1771 ---
obs0.178 140419 96.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 100.47 Å2 / Biso mean: 33.996 Å2 / Biso min: 7.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 1.95→81.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10224 0 354 1145 11723
Biso mean--56.7 37.56 -
Num. residues----1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911065
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210198
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.94115186
X-RAY DIFFRACTIONr_angle_other_deg0.929323457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0351332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88622.126522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.791151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.85215121
X-RAY DIFFRACTIONr_chiral_restr0.0810.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112255
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022600
X-RAY DIFFRACTIONr_mcbond_it0.8571.8655241
X-RAY DIFFRACTIONr_mcbond_other0.8561.8645240
X-RAY DIFFRACTIONr_mcangle_it1.3842.7926566
Refine LS restraints NCS

Ens-ID: 1 / Number: 43810 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 418 -
Rwork0.349 8305 -
all-8723 -
obs--78.86 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7104-0.0350.21860.3727-0.19295.14070.02920.13440.0442-0.024-0.0796-0.0720.04830.18860.05040.03060.050.02130.10350.02870.0654-17.4221-37.738168.0936
20.3897-0.1391-1.09580.4408-0.00183.4835-0.07950.1086-0.0418-0.2078-0.1816-0.1550.468-0.14610.26110.17150.04460.08110.24920.02730.1895-8.8242-46.700153.4447
30.9594-0.385-0.5652.8075-0.13731.18980.0278-0.1357-0.00180.3608-0.0994-0.0581-0.12360.11590.07160.1298-0.0416-0.04490.03150.01150.0204-22.0701-34.2584113.6615
40.87950.1405-0.24981.5053-0.42741.6564-0.04660.1657-0.201-0.1512-0.02610.08860.381-0.1540.07270.1167-0.0339-0.00180.0433-0.04460.062-29.9505-52.550295.4962
50.3066-0.171-0.03760.83290.03995.11950.01580.06590.0440.0317-0.0198-0.0425-0.1606-0.01780.0040.05140.037-0.0140.0438-0.01550.0484-37.8307-17.382780.9011
60.4946-0.1321-0.7410.42261.19813.9703-0.0013-0.12060.09540.0372-0.08250.0633-0.1276-0.12830.08380.18220.0080.01550.0789-0.0120.125-46.7693-8.993494.7283
73.7135-1.0468-0.35181.28980.71111.0551-0.03730.3545-0.0488-0.1243-0.04360.0156-0.09860.06220.08090.0194-0.0184-0.00280.1890.02550.013-35.7569-23.008933.3278
81.6188-0.09710.45290.88820.16551.4173-0.0511-0.1613-0.16470.1402-0.00280.18120.1089-0.30490.05390.0326-0.00140.03560.1481-0.00360.0534-49.7315-28.544852.3596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 115
2X-RAY DIFFRACTION2A116 - 213
3X-RAY DIFFRACTION3A214 - 395
4X-RAY DIFFRACTION4A396 - 662
5X-RAY DIFFRACTION5B15 - 115
6X-RAY DIFFRACTION6B116 - 214
7X-RAY DIFFRACTION7B215 - 361
8X-RAY DIFFRACTION8B362 - 662

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