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- PDB-9i2j: Branching Sucrase BRS-B in complex with Sucrose -

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Basic information

Entry
Database: PDB / ID: 9i2j
TitleBranching Sucrase BRS-B in complex with Sucrose
Componentsdextransucrase
KeywordsHYDROLASE / GH70 / Branching / Sucrase / Dextran
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity
Similarity search - Function
Glucan-binding repeat / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat ...Glucan-binding repeat / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Cell wall/choline-binding repeat / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-fructofuranose / alpha-D-glucopyranose / dextransucrase
Similarity search - Component
Biological speciesLeuconostoc citreum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCioci, G. / Benkoulouche, M. / Claverie, M. / Remaud-Simeon, M. / Moulis, C. / Guieysse, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Branching Sucrase BRS-B in complex with Sucrose
Authors: Cioci, G.
History
DepositionJan 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dextransucrase
B: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,41912
Polymers264,8172
Non-polymers4,60210
Water3,333185
1
A: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,6296
Polymers132,4091
Non-polymers2,2205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,7916
Polymers132,4091
Non-polymers2,3825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)255.133, 255.133, 344.915
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 1164 / Label seq-ID: 3 - 1164

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein dextransucrase / Dextransucrase / Sucrose 6-glucosyltransferase


Mass: 132408.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc citreum (bacteria) / Gene: LCIT_06060 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5A5U0V5, dextransucrase

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Sugars , 5 types, 8 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1477.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,9,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1_e6-f1_f6-g1_g6-h1_h6-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 187 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.08 Å3/Da / Density % sol: 69.85 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 0.1M SPG Buffer pH 7, 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.1→48.63 Å / Num. obs: 76886 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.982 / Net I/σ(I): 4.4
Reflection shellResolution: 3.1→3.27 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1 / Num. unique obs: 37306

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.262 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.1 / SU ML: 0.301 / Cross valid method: FREE R-VALUE / ESU R Free: 0.361
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2253 3803 4.947 %
Rwork0.1925 73078 -
all0.194 --
obs-76881 98.502 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.054 Å2
Baniso -1Baniso -2Baniso -3
1-1.375 Å20.688 Å20 Å2
2--1.375 Å20 Å2
3----4.462 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18161 0 301 185 18647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01218868
X-RAY DIFFRACTIONr_bond_other_d0.0010.01617075
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.79625623
X-RAY DIFFRACTIONr_angle_other_deg0.4711.7739346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.32652303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.672547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.558103063
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.13210968
X-RAY DIFFRACTIONr_chiral_restr0.0610.22824
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024402
X-RAY DIFFRACTIONr_nbd_refined0.2130.23644
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.216350
X-RAY DIFFRACTIONr_nbtor_refined0.180.29433
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.210071
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2348
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.10.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.220
X-RAY DIFFRACTIONr_nbd_other0.1880.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.24
X-RAY DIFFRACTIONr_mcbond_it3.8786.5259231
X-RAY DIFFRACTIONr_mcbond_other3.8786.5259231
X-RAY DIFFRACTIONr_mcangle_it6.27611.72711525
X-RAY DIFFRACTIONr_mcangle_other6.27611.72611526
X-RAY DIFFRACTIONr_scbond_it4.026.7919637
X-RAY DIFFRACTIONr_scbond_other4.026.7919638
X-RAY DIFFRACTIONr_scangle_it6.70412.36414098
X-RAY DIFFRACTIONr_scangle_other6.70412.36314099
X-RAY DIFFRACTIONr_lrange_it11.05378.23279600
X-RAY DIFFRACTIONr_lrange_other11.05378.2479576
X-RAY DIFFRACTIONr_ncsr_local_group_10.1050.0537084
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.104950.05012
12AX-RAY DIFFRACTIONLocal ncs0.104950.05012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.1-3.180.3423020.32653920.32757130.9140.92399.66740.313
3.18-3.2670.3492650.31152390.31355380.9240.93199.38610.295
3.267-3.3610.2882380.29551510.29554140.9370.93999.53820.276
3.361-3.4640.2852510.26349910.26552720.9450.95399.4310.239
3.464-3.5770.2972380.24548140.24750890.9370.9699.27290.221
3.577-3.7020.2642240.23846600.23949340.9470.96498.98660.215
3.702-3.8410.2732370.21444500.21747690.9520.97198.28060.195
3.841-3.9970.2612040.19643210.19945960.9610.97698.45520.176
3.997-4.1730.2122240.18141380.18344120.970.97998.86670.158
4.173-4.3750.1852020.15539740.15742290.9780.98598.74670.137
4.375-4.610.1912230.1437430.14240210.9770.98798.63220.124
4.61-4.8860.172010.1435470.14238130.9840.98898.29530.124
4.886-5.220.1861690.13533580.13835990.9810.98997.99940.12
5.22-5.6330.181410.14931480.15133410.9820.98898.44360.135
5.633-6.1620.2141630.1728800.17230920.9730.98498.41530.153
6.162-6.8750.2071550.15726120.1628270.9770.98697.87760.143
6.875-7.9120.1851300.14122740.14424940.9790.98796.39130.129
7.912-9.6260.1521150.13419380.13521380.9840.9996.02430.128
9.626-13.350.173780.14815240.1516950.9860.9994.51330.144
13.35-48.2620.178430.2029240.20110350.9840.97993.430.2

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