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- PDB-5e6y: Crystal structure of E.Coli branching enzyme in complex with alph... -

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Basic information

Entry
Database: PDB / ID: 5e6y
TitleCrystal structure of E.Coli branching enzyme in complex with alpha cyclodextrin
Components1,4-alpha-glucan branching enzyme GlgB
KeywordsTRANSFERASE / branching enzyme / cyclodextrin / glycogen / starch / glucan
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / starch metabolic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytosol
Similarity search - Function
Glycogen branching enzyme GlgB, N-terminal Early set domain / 1,4-alpha-glucan-branching enzyme, GlgB / 1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Glycogen branching enzyme GlgB, N-terminal Early set domain / 1,4-alpha-glucan-branching enzyme, GlgB / 1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-cyclodextrin / 1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFeng, L. / Nosrati, M. / Geiger, J.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Crystal structures of Escherichia coli branching enzyme in complex with cyclodextrins.
Authors: Feng, L. / Fawaz, R. / Hovde, S. / Sheng, F. / Nosrati, M. / Geiger, J.H.
History
DepositionOct 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
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 / pdbx_struct_oper_list / 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.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: 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: 1,4-alpha-glucan branching enzyme GlgB
B: 1,4-alpha-glucan branching enzyme GlgB
C: 1,4-alpha-glucan branching enzyme GlgB
D: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,48918
Polymers285,1114
Non-polymers9,37814
Water10,467581
1
A: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4445
Polymers71,2781
Non-polymers2,1664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4534
Polymers71,2781
Non-polymers1,1753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2504
Polymers71,2781
Non-polymers2,9733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3425
Polymers71,2781
Non-polymers3,0654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.024, 103.808, 186.080
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
1,4-alpha-glucan branching enzyme GlgB / 1 / 4-alpha-D-glucan:1 / 4-alpha-D-glucan 6-glucosyl-transferase / Alpha-(1->4)-glucan branching ...1 / 4-alpha-D-glucan:1 / 4-alpha-D-glucan 6-glucosyl-transferase / Alpha-(1->4)-glucan branching enzyme / Glycogen branching enzyme / BE


Mass: 71277.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: glgB, EcE24377A_3911 / Production host: Escherichia coli (E. coli)
References: UniProt: A7ZSW5, 1,4-alpha-glucan branching enzyme
#2: Polysaccharide
Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 9
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1M HEPES, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97876 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / % possible obs: 95 % / Redundancy: 4 % / Net I/σ(I): 25

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M7X

1m7x


Resolution: 2.6→42.431 Å / SU ML: 0.77 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 10356 10.05 %RANDOM
Rwork0.1904 ---
obs0.1971 103070 95.17 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.542 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0225 Å20 Å2-1.1767 Å2
2--1.0683 Å20 Å2
3----2.0908 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19246 0 624 581 20451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00920541
X-RAY DIFFRACTIONf_angle_d1.26728002
X-RAY DIFFRACTIONf_dihedral_angle_d16.9247076
X-RAY DIFFRACTIONf_chiral_restr0.0872972
X-RAY DIFFRACTIONf_plane_restr0.0053538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5961-2.62560.34642980.28242822X-RAY DIFFRACTION86
2.6256-2.65650.36223230.26163046X-RAY DIFFRACTION94
2.6565-2.68880.33033310.24832977X-RAY DIFFRACTION93
2.6888-2.72290.31943160.24083087X-RAY DIFFRACTION93
2.7229-2.75870.35753370.2413011X-RAY DIFFRACTION94
2.7587-2.79650.27723390.23013063X-RAY DIFFRACTION94
2.7965-2.83640.34583450.24613056X-RAY DIFFRACTION95
2.8364-2.87870.3443250.23573011X-RAY DIFFRACTION93
2.8787-2.92370.31813550.23823055X-RAY DIFFRACTION96
2.9237-2.97160.3453210.23173071X-RAY DIFFRACTION94
2.9716-3.02290.30613320.21873052X-RAY DIFFRACTION95
3.0229-3.07780.29033670.20923043X-RAY DIFFRACTION94
3.0778-3.1370.29113560.20333074X-RAY DIFFRACTION95
3.137-3.2010.29893940.21143013X-RAY DIFFRACTION95
3.201-3.27060.29833190.20883104X-RAY DIFFRACTION96
3.2706-3.34660.28993460.20813130X-RAY DIFFRACTION96
3.3466-3.43030.28973390.19333070X-RAY DIFFRACTION95
3.4303-3.5230.25423600.18973086X-RAY DIFFRACTION95
3.523-3.62660.2583370.18823105X-RAY DIFFRACTION96
3.6266-3.74360.24893670.1763118X-RAY DIFFRACTION96
3.7436-3.87730.23693410.17313093X-RAY DIFFRACTION95
3.8773-4.03240.24263640.17113076X-RAY DIFFRACTION95
4.0324-4.21580.22043310.16453122X-RAY DIFFRACTION95
4.2158-4.43790.22483490.15993038X-RAY DIFFRACTION94
4.4379-4.71560.2243580.15613068X-RAY DIFFRACTION95
4.7156-5.07910.20483390.15123179X-RAY DIFFRACTION97
5.0791-5.58920.21843670.16613224X-RAY DIFFRACTION99
5.5892-6.39560.23513540.19053278X-RAY DIFFRACTION100
6.3956-8.04880.2543480.19823327X-RAY DIFFRACTION100
8.0488-42.43680.22433980.20023315X-RAY DIFFRACTION99

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