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- PDB-3zst: GlgE isoform 1 from Streptomyces coelicolor with alpha-cyclodextr... -

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Basic information

Entry
Database: PDB / ID: 3zst
TitleGlgE isoform 1 from Streptomyces coelicolor with alpha-cyclodextrin bound
ComponentsPUTATIVE GLUCANOHYDROLASE PEP1A GLGE ISOFORM 1
KeywordsHYDROLASE / ALPHA-GLUCAN BIOSYNTHESIS / GLYCOSIDE HYDROLASE FAMILY 13_3
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
: / 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 / Golgi alpha-mannosidase II / 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 / 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-cyclodextrin / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSyson, K. / Stevenson, C.E.M. / Rejzek, M. / Fairhurst, S.A. / Nair, A. / Bruton, C.J. / Field, R.A. / Chater, K.F. / Lawson, D.M. / Bornemann, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of a Streptomyces Maltosyltransferase Glge: A Homologue of a Genetically Validated Anti-Tuberculosis Target.
Authors: Syson, K. / Stevenson, C.E.M. / Rejzek, M. / Fairhurst, S.A. / Nair, A. / Bruton, C.J. / Field, R.A. / Chater, K.F. / Lawson, D.M. / Bornemann, S.
History
DepositionJun 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Nov 9, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE GLUCANOHYDROLASE PEP1A GLGE ISOFORM 1
B: PUTATIVE GLUCANOHYDROLASE PEP1A GLGE ISOFORM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,1735
Polymers155,1302
Non-polymers2,0443
Water13,169731
1
B: PUTATIVE GLUCANOHYDROLASE PEP1A GLGE ISOFORM 1
hetero molecules

B: PUTATIVE GLUCANOHYDROLASE PEP1A GLGE ISOFORM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,1114
Polymers155,1302
Non-polymers1,9822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area5620 Å2
ΔGint-27.5 kcal/mol
Surface area52490 Å2
MethodPISA
2
A: PUTATIVE GLUCANOHYDROLASE PEP1A GLGE ISOFORM 1
hetero molecules

A: PUTATIVE GLUCANOHYDROLASE PEP1A GLGE ISOFORM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,2366
Polymers155,1302
Non-polymers2,1064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6030 Å2
ΔGint-15.1 kcal/mol
Surface area52080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.240, 113.240, 314.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 15 - 663 / Label seq-ID: 35 - 683

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein PUTATIVE GLUCANOHYDROLASE PEP1A GLGE ISOFORM 1 / GLGE ISOFORM 1 / PEP1A / SCO5443 / 1-4-ALPHA-D-


Mass: 77564.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: M145 / Plasmid: PET15B-GLGE1-M145 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q9L1K2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Polysaccharide Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,6,6/[a2122h-1a_1-5]/1-1-1-1-1-1/a1-f4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsETHYLENE GLYCOL (EDO): USED IN THE CRYOPROTECTANT
Sequence detailsINCLUDES AN ADDITIONAL 20 RESIDUES AT THE N-TERMINUS FOR NICKEL AFFINITY PURIFICATION.

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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: 62.8 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→71.35 Å / Num. obs: 85772 / % possible obs: 93.7 % / Observed criterion σ(I): -9 / Redundancy: 14.3 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 7.9 / % possible all: 66

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
PHASERphasing
REFMAC5.6.0101refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEMET DERIVATIVE MODEL SOLVED BY MAD

Resolution: 2.3→106.54 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.303 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.20132 4301 5 %RANDOM
Rwork0.17257 ---
obs0.17401 81357 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→106.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10239 0 136 731 11106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210770
X-RAY DIFFRACTIONr_bond_other_d0.0040.027402
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.97114763
X-RAY DIFFRACTIONr_angle_other_deg1.133.00117692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01151315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05122.282517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.877151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.18315115
X-RAY DIFFRACTIONr_chiral_restr0.0890.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112013
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022358
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24469 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 163 -
Rwork0.195 3635 -
obs--58.8 %
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)
11.2079-0.3868-0.37190.53210.15397.22640.01280.12460.0150.13160.02050.02760.0392-0.1972-0.03330.04690.01030.01310.0877-0.00470.182811.119731.9227-2.1467
21.9537-0.8341.61246.4479-2.93877.091-0.0498-0.23390.18780.43720.14520.1276-0.4549-0.0649-0.09540.12740.0214-0.00410.2384-0.01890.2734-0.608747.2681-23.2577
30.1887-0.5123-0.4911.46661.549620.78070.0393-0.09140.09780.02090.333-0.30810.7587-0.4097-0.37220.0719-0.0005-0.04160.1999-0.0050.1538.677727.01740.9477
40.44660.0309-0.09541.67520.11520.90010.0354-0.02-0.02440.202-0.0043-0.0420.0226-0.0165-0.03110.170.00390.01830.00170.00290.1124.009530.490733.3443
52.60151.30720.32612.83451.14872.2866-0.03720.34150.482-0.47050.04070.0272-0.6969-0.085-0.00360.47250.02960.08070.06630.06330.250827.14857.894614.6555
61.3034-0.69560.06391.15210.14827.6182-0.0521-0.2030.00570.06920.12390.1346-0.0276-0.8218-0.07180.16340.0339-0.02690.4640.01510.2153-41.389292.0143-4.0171
73.3353-0.38070.9654.1405-1.76855.1965-0.2509-0.30670.21920.33590.05060.1185-0.3107-0.25660.20030.30670.0374-0.05570.3698-0.04520.3386-52.4584104.4101-26.773
82.27280.49525.8123.75915.030519.02170.19310.00530.160.7159-0.65760.10031.673-0.68690.46450.4465-0.21510.07440.67770.06890.2331-43.99487.3479-0.6336
90.68250.0129-0.07321.69750.24081.6950.0167-0.16990.0040.136-0.04670.0117-0.1265-0.36480.030.22640.038-0.01050.34-0.01040.2058-31.97993.713332.7696
104.10320.62251.45033.28490.7594.0294-0.24410.28050.8342-0.6175-0.0302-0.0991-1.2799-0.2490.27430.92290.1111-0.02260.32490.04970.4445-26.356119.375512.6067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 108
2X-RAY DIFFRACTION2A109 - 192
3X-RAY DIFFRACTION3A193 - 205
4X-RAY DIFFRACTION4A206 - 573
5X-RAY DIFFRACTION5A574 - 663
6X-RAY DIFFRACTION6B15 - 108
7X-RAY DIFFRACTION7B109 - 192
8X-RAY DIFFRACTION8B193 - 205
9X-RAY DIFFRACTION9B206 - 573
10X-RAY DIFFRACTION10B574 - 663

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