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- PDB-5lgv: GlgE isoform 1 from Streptomyces coelicolor E423A mutant soaked i... -

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Basic information

Entry
Database: PDB / ID: 5lgv
TitleGlgE isoform 1 from Streptomyces coelicolor E423A mutant soaked in maltooctaose
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsTRANSFERASE / hydrolase / alpha-glucan biosynthesis / glycoside hydrolase family 13_3
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / oligosaccharide catabolic process / hexosyltransferase activity / 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 / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...: / 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 / 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-maltopentaose / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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 1.4Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)159,3016
Polymers155,0142
Non-polymers4,2884
Water8,053447
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13200 Å2
ΔGint64 kcal/mol
Surface area50620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.611, 113.611, 313.692
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: 77506.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: E423A 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 (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: glgE1, pep1, pep1A, pep1I, SCO5443, SC6A11.19c / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q9L1K2, starch synthase (maltosyl-transferring)
#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-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1315.142 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,8,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 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]{[(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 / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 3.27 Å3/Da / Density % sol: 62.33 % / 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: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→49.92 Å / Num. obs: 72101 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 50.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/av σ(I): 17.9 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.5-2.568.20.9042.30.6281100
11.18-49.9213.50.0310.999199

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
REFMACphasing
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4CN6

4cn6


Resolution: 2.5→49.92 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 16.796 / SU ML: 0.185 / SU R Cruickshank DPI: 0.3029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.212
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 3560 4.9 %RANDOM
Rwork0.179 ---
obs0.1805 68441 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.66 Å2 / Biso mean: 65.669 Å2 / Biso min: 30.13 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å20 Å2
2--2.56 Å20 Å2
3----5.12 Å2
Refinement stepCycle: final / Resolution: 2.5→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10144 0 290 447 10881
Biso mean--93.32 53.79 -
Num. residues----1298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910834
X-RAY DIFFRACTIONr_bond_other_d0.0020.029927
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.93414883
X-RAY DIFFRACTIONr_angle_other_deg0.948322813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24351314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3422.39498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.227151526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2415103
X-RAY DIFFRACTIONr_chiral_restr0.0750.21704
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022527
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.282.1335208
X-RAY DIFFRACTIONr_mcbond_other1.2782.1325207
X-RAY DIFFRACTIONr_mcangle_it2.0983.1956511
X-RAY DIFFRACTIONr_mcangle_other2.0983.1966512
X-RAY DIFFRACTIONr_scbond_it2.2742.6555626
X-RAY DIFFRACTIONr_scbond_other2.2742.6575627
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.473.9378364
X-RAY DIFFRACTIONr_long_range_B_refined8.60928.44411773
X-RAY DIFFRACTIONr_long_range_B_other8.60327.68811623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 274 -
Rwork0.314 4966 -
all-5240 -
obs--99.96 %
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)
11.50730.11090.38510.31490.23626.7609-0.00110.2856-0.014-0.1134-0.1061-0.09210.4060.49130.10720.40510.13040.11510.237-0.00890.456542.6042-32.1084-4.9192
21.3335-0.431-2.39570.16380.75114.3998-0.4649-0.1502-0.13660.03370.088-0.00161.03570.45190.3770.87770.23440.16520.9317-0.20240.792152.1653-42.8038-17.3091
30.9242-0.8728-0.39244.2212-0.15171.8999-0.028-0.14290.06630.37970.0034-0.0483-0.07850.03540.02450.4895-0.0396-0.02010.052-0.03350.377234.7714-22.582439.2535
41.16790.18980.17792.318-0.99752.19260.17770.1221-0.2271-0.239-0.02870.12780.594-0.0584-0.1490.52930.019-0.02090.0207-0.01990.435528.883-43.283222.7329
51.4095-0.1849-0.25831.62560.27516.9547-0.05230.05690.01260.0042-0.1420.0602-0.1346-0.18610.19430.35240.04520.00320.0337-0.07140.424921.105-10.28423.8364
60.3428-0.6181-0.97381.39442.64416.26440.0938-0.02450.082-0.0917-0.29320.1265-0.3459-1.41730.19940.5340.080.08690.6613-0.06230.70811.1518-0.948116.1662
74.8002-0.809-0.13781.29120.47622.0677-0.04410.3831-0.1776-0.3648-0.0586-0.01220.03320.01450.10270.582-0.03490.03930.3882-0.08440.400725.6114-23.374-42.1945
81.622-0.10080.95911.30070.31782.7766-0.0451-0.1367-0.2159-0.0282-0.07080.26320.1134-0.81220.11590.416-0.00210.01030.4279-0.11160.484311.1968-25.3267-22.9884
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 - 663
5X-RAY DIFFRACTION5B15 - 115
6X-RAY DIFFRACTION6B116 - 214
7X-RAY DIFFRACTION7B215 - 361
8X-RAY DIFFRACTION8B362 - 663

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