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- PDB-9ibt: Branching Sucrase Brs-B in complex with isomaltopentaose in the a... -

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Basic information

Entry
Database: PDB / ID: 9ibt
TitleBranching Sucrase Brs-B in complex with isomaltopentaose in the active site (alternative conformation)
Componentsdextransucrase
KeywordsCYTOSOLIC PROTEIN / Glucansucrase / dextran / GH70 / branching
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
Biological speciesLeuconostoc citreum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsCioci, G. / Moulis, C. / Claverie, M. / Benkholouche, M. / Remaud-Simeon, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Brs-B
Authors: Cioci, G.
History
DepositionFeb 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 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)272,03213
Polymers264,8172
Non-polymers7,21411
Water19811
1
A: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,1067
Polymers132,4091
Non-polymers3,6976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9266
Polymers132,4091
Non-polymers3,5175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)253.639, 253.639, 344.433
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: 153 - 1314 / 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, 9 molecules

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


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
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
[][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-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a6-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: 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


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][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
#5: 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
[][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]{[(6+1)][a-D-Glcp]{}}}}}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
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
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 13 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.03 Å3/Da / Density % sol: 69.45 %
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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 63973 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 3.7
Reflection shellResolution: 3.3→3.48 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 9290 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.412 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.892 / SU B: 20.174 / SU ML: 0.316 / Cross valid method: FREE R-VALUE / ESU R Free: 0.418
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2252 3137 4.904 %
Rwork0.2007 60834 -
all0.202 --
obs-63971 99.947 %
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: 66.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.755 Å20.378 Å20 Å2
2--0.755 Å20 Å2
3----2.45 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18147 0 484 11 18642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01219054
X-RAY DIFFRACTIONr_bond_other_d0.0010.01617142
X-RAY DIFFRACTIONr_angle_refined_deg0.91.79825910
X-RAY DIFFRACTIONr_angle_other_deg0.3931.76739564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62252301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.144546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.951103048
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.4110972
X-RAY DIFFRACTIONr_chiral_restr0.0450.22910
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0222365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024399
X-RAY DIFFRACTIONr_nbd_refined0.2060.23640
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.216799
X-RAY DIFFRACTIONr_nbtor_refined0.1750.29498
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.29623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2435
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.215
X-RAY DIFFRACTIONr_nbd_other0.180.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0740.24
X-RAY DIFFRACTIONr_mcbond_it1.3786.7569223
X-RAY DIFFRACTIONr_mcbond_other1.3786.7569223
X-RAY DIFFRACTIONr_mcangle_it2.48112.14711515
X-RAY DIFFRACTIONr_mcangle_other2.48112.14711516
X-RAY DIFFRACTIONr_scbond_it1.1456.8799831
X-RAY DIFFRACTIONr_scbond_other1.1456.8799832
X-RAY DIFFRACTIONr_scangle_it2.12312.65314395
X-RAY DIFFRACTIONr_scangle_other2.12312.65314396
X-RAY DIFFRACTIONr_lrange_it5.55480.80380036
X-RAY DIFFRACTIONr_lrange_other5.55480.80380037
X-RAY DIFFRACTIONr_ncsr_local_group_10.1040.0537430
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.103810.05012
12AX-RAY DIFFRACTIONLocal ncs0.103810.05012
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
3.3-3.3850.3092510.31644600.31647120.9460.94299.97880.284
3.385-3.4780.3082260.27943120.2845380.9390.9511000.253
3.478-3.5780.2412190.24842500.24844690.960.961000.223
3.578-3.6870.2572080.24240640.24342720.9610.9621000.22
3.687-3.8080.2721930.23339680.23441610.9520.9671000.212
3.808-3.940.2422080.22138350.22240430.9590.971000.202
3.94-4.0880.2471770.21237490.21339270.9650.97299.97450.195
4.088-4.2540.2011710.19535940.19537650.9740.9761000.18
4.254-4.4410.2031770.17934370.1836140.9730.981000.166
4.441-4.6560.1921790.16732710.16834500.9750.9821000.154
4.656-4.9050.1911420.16531520.16732940.9770.9831000.154
4.905-5.20.2261280.16729970.16931250.9720.9821000.154
5.2-5.5540.2121710.1827700.18129430.9760.98199.9320.167
5.554-5.9930.2121490.20125920.20227410.9720.9781000.185
5.993-6.5540.2131430.19723990.19825420.9730.9771000.183
6.554-7.3110.2121070.17522020.17723090.9720.9811000.166
7.311-8.4110.1731000.16119560.16220560.980.9841000.158
8.411-10.2240.187840.14716730.14917570.9760.9871000.149
10.224-14.1470.156640.15513320.15513960.9810.9871000.159
14.147-48.4120.288400.258210.2528630.9330.94699.76820.265

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