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- PDB-5e70: Crystal structure of Ecoli Branching Enzyme with gamma cyclodextrin -

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Basic information

Entry
Database: PDB / ID: 5.0E+70
TitleCrystal structure of Ecoli Branching Enzyme with gamma cyclodextrin
Components1,4-alpha-glucan branching enzyme GlgB
KeywordsTRANSFERASE / Branching Enzyme / Cyclodextrin / Glycogen / Starch / glucan
Function / homology
Function and homology information


1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) / 1,4-alpha-glucan branching enzyme activity / cation binding / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds
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
gamma-cyclodextrin / 1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_symm_contact / 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.occupancy / _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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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)292,23915
Polymers285,1114
Non-polymers7,12811
Water21,7081205
1
A: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7774
Polymers71,2781
Non-polymers1,4993
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)72,7774
Polymers71,2781
Non-polymers1,4993
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)72,5932
Polymers71,2781
Non-polymers1,3151
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)74,0925
Polymers71,2781
Non-polymers2,8144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.097, 103.221, 186.694
Angle α, β, γ (deg.)90.00, 91.73, 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
Cyclooctakis-(1-4)-(alpha-D-glucopyranose) / gamma-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1315.142 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: gamma-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,8,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a1-h4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1205 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
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: 0.9788 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: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 126463 / % possible obs: 95 % / Redundancy: 4 % / Net I/σ(I): 25

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M7X

1m7x


Resolution: 2.33→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.56 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21716 14049 10 %RANDOM
Rwork0.1703 ---
obs0.17504 126463 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.039 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.13 Å2
2---0.45 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19341 0 476 1205 21022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02120591
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.94728041
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1952363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27522.981104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.373153120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.50215169
X-RAY DIFFRACTIONr_chiral_restr0.10.22918
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116047
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.041211732
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.752318821
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2128859
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8339219
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
LS refinement shellResolution: 2.334→2.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 936 -
Rwork0.211 8799 -
obs--88.63 %
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)
12.0771.41310.13341.37560.39875.1308-0.64550.8261-0.5403-0.69780.3-0.22210.1687-0.02940.34560.3955-0.08370.09910.4957-0.30040.206932.887331.466631.1565
20.87140.0062-0.30990.5623-0.18970.9161-0.05780.1731-0.2386-0.20020.00810.09790.1418-0.06440.04970.1378-0.024-0.03060.1645-0.03190.244521.614939.175467.2794
31.577-0.38970.50931.4286-0.81141.61880.0535-0.1372-0.1951-0.0364-0.0459-0.11310.08810.0654-0.00760.04590.0002-0.00430.16070.10580.329774.687222.590191.4787
40.856-0.21890.03030.7555-0.1640.2153-0.0021-0.1464-0.0413-0.02080.0077-0.07430.00060.0361-0.00550.1262-0.01290.0040.2350.01490.171455.853455.214280.6667
51.2738-0.1991-1.34884.04422.50082.7889-0.1065-0.0202-0.15870.02460.1448-0.24130.21430.2313-0.03830.30560.2472-0.03140.2847-0.10550.094892.511945.1576-3.3613
61.2470.14120.05590.97870.51191.57670.02980.0543-0.06170.05840.042-0.19730.18550.3476-0.07170.20070.05410.03030.18640.00930.101788.635171.538825.8984
71.3705-0.4020.73682.5874-1.39411.4177-0.0251-0.05540.0152-0.20840.0202-0.0952-0.10760.01820.00490.4550.02870.05190.09370.03770.063745.177104.9348-2.5867
80.4773-0.0422-0.00220.6809-0.37881.11270.0315-0.02790.0322-0.1095-0.0017-0.0089-0.0046-0.0413-0.02970.3166-0.01440.01150.1383-0.00110.106549.388876.645325.6415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A117 - 233
2X-RAY DIFFRACTION2A234 - 728
3X-RAY DIFFRACTION3B117 - 229
4X-RAY DIFFRACTION4B230 - 728
5X-RAY DIFFRACTION5C118 - 232
6X-RAY DIFFRACTION6C233 - 727
7X-RAY DIFFRACTION7D117 - 226
8X-RAY DIFFRACTION8D227 - 728

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