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- PDB-21kg: Faecalibacterium duncaniae branching enzyme FdBE2 maltohexaose complex -

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Basic information

Entry
Database: PDB / ID: 21kg
TitleFaecalibacterium duncaniae branching enzyme FdBE2 maltohexaose complex
Components1,4-alpha-glucan branching enzyme
KeywordsTRANSFERASE / Branching enzyme / GH13_9 / Transglucosylation
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytosol
Similarity search - Function
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 ...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 / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-maltohexaose / 1,4-alpha-glucan branching enzyme
Similarity search - Component
Biological speciesFaecalibacterium duncaniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTonozuka, T. / Ding, Y. / Sugimura, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K08698 Japan
Japan Society for the Promotion of Science (JSPS)24KJ1029 Japan
CitationJournal: To Be Published
Title: Enzymatic and structural and characterization of a branching enzyme FdBE2 from the gut bacterium Faecalibacterium duncaniae
Authors: Ding, Y. / Sugimura, R. / Suzuki, R. / Endo, A. / Nishikawa, A. / Kozono, T. / Tonozuka, T.
History
DepositionDec 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,63410
Polymers73,1581
Non-polymers2,4769
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint16 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.395, 73.476, 56.971
Angle α, β, γ (deg.)90.00, 91.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 1,4-alpha-glucan branching enzyme


Mass: 73157.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Expression tag, MGSSHHHHHHSSGLVPRGSH Amino acid residues 618-647 is removed.
Source: (gene. exp.) Faecalibacterium duncaniae (bacteria) / Strain: JCM31915 / Gene: glgB, FAEPRAA2165_01813 / Production host: Escherichia coli (E. coli)
References: UniProt: C7H686, 1,4-alpha-glucan branching enzyme
#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


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltohexaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG4000, PEG3350, ammonium sulfate, Tris-HCl pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.6 Å / Num. obs: 88773 / % possible obs: 98.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.023 / Rpim(I) all: 0.015 / Net I/σ(I): 19.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3850 / Rpim(I) all: 0.192 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.61 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16749 4359 4.9 %RANDOM
Rwork0.14848 ---
obs0.14942 84413 98.73 %-
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: 21.293 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4939 0 166 533 5638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135273
X-RAY DIFFRACTIONr_bond_other_d0.0350.0154573
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.6887166
X-RAY DIFFRACTIONr_angle_other_deg3.0261.61210548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8835605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36621.359309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56415757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8061537
X-RAY DIFFRACTIONr_chiral_restr0.0640.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025905
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021345
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_it1.2712.0812430
X-RAY DIFFRACTIONr_mcbond_other1.2712.082428
X-RAY DIFFRACTIONr_mcangle_it2.1863.1113031
X-RAY DIFFRACTIONr_mcangle_other2.1863.1123032
X-RAY DIFFRACTIONr_scbond_it1.6232.3212841
X-RAY DIFFRACTIONr_scbond_other1.6232.3212841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6063.424136
X-RAY DIFFRACTIONr_long_range_B_refined4.57725.2256242
X-RAY DIFFRACTIONr_long_range_B_other4.44824.8116136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 275 -
Rwork0.205 5722 -
obs--90.59 %

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