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- PDB-5e6z: Crystal structure of Ecoli Branching Enzyme with beta cyclodextrin -

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Basic information

Entry
Database: PDB / ID: 5e6z
TitleCrystal structure of Ecoli Branching Enzyme with beta 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 / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / alpha-1,4-glucan branching enzyme GlgB, N-terminal domain / 1,4-alpha-glucan-branching enzyme, GlgB / Glycogen branching enzyme GlgB, N-terminal Early set domain / 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 ...: / alpha-1,4-glucan branching enzyme GlgB, N-terminal domain / 1,4-alpha-glucan-branching enzyme, GlgB / Glycogen branching enzyme GlgB, N-terminal Early set domain / 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
beta-cyclodextrin / 1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.878 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.pdbx_synonyms / _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)292,67317
Polymers285,1114
Non-polymers7,56313
Water33,0941837
1
A: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7685
Polymers71,2781
Non-polymers2,4904
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)72,6154
Polymers71,2781
Non-polymers1,3373
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)73,6764
Polymers71,2781
Non-polymers2,3983
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)72,6154
Polymers71,2781
Non-polymers1,3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.952, 102.995, 186.239
Angle α, β, γ (deg.)90.00, 91.57, 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
Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1837 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.2 / Details: 0.1 M NaHEPES, 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 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 1.878→50 Å / % possible obs: 99.5 % / 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: 1.878→44.927 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 28009 9.97 %RANDOM
Rwork0.2064 ---
obs0.2106 280877 99.44 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.416 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3477 Å2-0 Å20.4643 Å2
2--0.3829 Å20 Å2
3----0.0352 Å2
Refinement stepCycle: LAST / Resolution: 1.878→44.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19305 0 504 1837 21646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720660
X-RAY DIFFRACTIONf_angle_d1.09528163
X-RAY DIFFRACTIONf_dihedral_angle_d15.797256
X-RAY DIFFRACTIONf_chiral_restr0.0772948
X-RAY DIFFRACTIONf_plane_restr0.0053588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8782-1.89950.35468630.30667668X-RAY DIFFRACTION91
1.8995-1.92190.34069120.28558388X-RAY DIFFRACTION99
1.9219-1.94530.32728980.27558500X-RAY DIFFRACTION100
1.9453-1.96990.30839790.25328357X-RAY DIFFRACTION100
1.9699-1.99580.29298930.2448487X-RAY DIFFRACTION100
1.9958-2.02320.29459570.24018380X-RAY DIFFRACTION100
2.0232-2.05210.28418800.23818535X-RAY DIFFRACTION100
2.0521-2.08270.27929580.23278383X-RAY DIFFRACTION100
2.0827-2.11530.27449370.23028429X-RAY DIFFRACTION100
2.1153-2.14990.26919710.22438481X-RAY DIFFRACTION100
2.1499-2.1870.26729650.22448462X-RAY DIFFRACTION100
2.187-2.22680.26549760.21838330X-RAY DIFFRACTION100
2.2268-2.26960.26668890.21558495X-RAY DIFFRACTION100
2.2696-2.31590.26558910.2138512X-RAY DIFFRACTION100
2.3159-2.36630.26419560.20978465X-RAY DIFFRACTION100
2.3663-2.42130.26379280.20868492X-RAY DIFFRACTION100
2.4213-2.48190.25529460.20368436X-RAY DIFFRACTION100
2.4819-2.5490.26789220.2088450X-RAY DIFFRACTION100
2.549-2.6240.24949220.20678519X-RAY DIFFRACTION100
2.624-2.70870.25359340.20338476X-RAY DIFFRACTION100
2.7087-2.80540.25159600.20848425X-RAY DIFFRACTION100
2.8054-2.91780.24599760.20968424X-RAY DIFFRACTION100
2.9178-3.05050.25579870.20188440X-RAY DIFFRACTION100
3.0505-3.21130.2449450.2038474X-RAY DIFFRACTION100
3.2113-3.41240.24759310.19868502X-RAY DIFFRACTION100
3.4124-3.67580.2279710.18728459X-RAY DIFFRACTION100
3.6758-4.04550.22049070.18078419X-RAY DIFFRACTION99
4.0455-4.63040.20979300.17558336X-RAY DIFFRACTION98
4.6304-5.83180.2238860.18588467X-RAY DIFFRACTION98
5.8318-44.93980.23399390.22128677X-RAY DIFFRACTION99

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