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- PDB-9sjh: Crystal structure of apo GHdex dextranase (BT3087), E360A catalyt... -

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Basic information

Entry
Database: PDB / ID: 9sjh
TitleCrystal structure of apo GHdex dextranase (BT3087), E360A catalytic mutant
ComponentsCycloisomaltooligosaccharide glucanotransferase
KeywordsSUGAR BINDING PROTEIN / dextran / Bacteroides / GH / glycoside hydrolase / enzyme / utilisome / GH66
Function / homologyGlycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Cycloisomaltooligosaccharide glucanotransferase
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFeasey, M. / Basle, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: J Struct Biol X / Year: 2026
Title: Structural and functional characterisation of the dextran utilisome from Bacteroides thetaiotaomicron
Authors: Feasey, M. / Silale, A. / Basle, A. / van den Berg, B.
History
DepositionAug 31, 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

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Assembly

Deposited unit
B: Cycloisomaltooligosaccharide glucanotransferase
A: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,20836
Polymers130,0152
Non-polymers3,19334
Water13,763764
1
B: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,66419
Polymers65,0081
Non-polymers1,65618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,54517
Polymers65,0081
Non-polymers1,53716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.862, 92.862, 330.684
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 27 - 593 / Label seq-ID: 4 - 570

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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

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Components

#1: Protein Cycloisomaltooligosaccharide glucanotransferase


Mass: 65007.520 Da / Num. of mol.: 2 / Mutation: E360A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3087
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A368
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2M ammonium sulphate 0.2M Potassium sodium tartrate 0.1M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→330.68 Å / Num. obs: 85740 / % possible obs: 100 % / Redundancy: 25.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.892 / Rpim(I) all: 0.251 / Rrim(I) all: 0.927 / Χ2: 0.96 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
11.11-330.6821.20.12415.67370.9890.0340.1290.8
2.1-2.1424.71.244600.75.02117.9050.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Aimlessdata scaling
DIALSdata reduction
MrBUMPphasing
PARROTphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→89.404 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.059 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.199 / ESU R Free: 0.172 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2295 4260 4.98 %
Rwork0.1903 81282 -
all0.192 --
obs-85542 99.931 %
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: 40.846 Å2
Baniso -1Baniso -2Baniso -3
1-1.261 Å2-0 Å2-0 Å2
2--1.261 Å2-0 Å2
3----2.522 Å2
Refinement stepCycle: LAST / Resolution: 2.1→89.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9020 0 166 764 9950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129390
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.80712780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12451136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.286532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.058101482
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.80610458
X-RAY DIFFRACTIONr_chiral_restr0.1120.21373
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027314
X-RAY DIFFRACTIONr_nbd_refined0.2380.24723
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2829
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3450.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.220
X-RAY DIFFRACTIONr_mcbond_it3.093.6154550
X-RAY DIFFRACTIONr_mcangle_it4.286.4755684
X-RAY DIFFRACTIONr_scbond_it5.5284.0934840
X-RAY DIFFRACTIONr_scangle_it7.9217.2747096
X-RAY DIFFRACTIONr_lrange_it26.18243.77114970
X-RAY DIFFRACTIONr_ncsr_local_group_10.0640.0519141
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.063630.05009
12AX-RAY DIFFRACTIONLocal ncs0.063630.05009
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
2.1-2.1550.3322930.30259090.30462170.9130.92299.75870.293
2.155-2.2140.3052870.28257720.28360700.9250.93799.81880.274
2.214-2.2780.2792900.25555990.25658960.9420.95199.88130.246
2.278-2.3480.2672890.24254540.24357500.950.95899.87830.231
2.348-2.4250.2922760.23252760.23555560.9450.96499.9280.219
2.425-2.510.2822720.23151510.23354260.9450.96499.94470.217
2.51-2.6040.3042720.23249100.23551850.9410.96699.94210.215
2.604-2.7110.3022370.22347920.22650300.9450.96999.98010.204
2.711-2.8310.2322390.21245950.21348350.9640.97199.97930.193
2.831-2.9690.2782320.21243940.21546260.950.9711000.193
2.969-3.1290.2842140.21542060.21844200.9440.971000.197
3.129-3.3190.2282110.18539840.18841960.9670.97999.97620.173
3.319-3.5480.1892070.15337420.15539500.9810.98699.97470.144
3.548-3.8320.1721990.13234840.13436840.9830.9999.97290.126
3.832-4.1970.1751970.12632360.12934330.9850.9911000.123
4.197-4.6910.1541570.1229560.12231130.9870.9911000.119
4.691-5.4140.1821440.14426320.14627760.980.9881000.145
5.414-6.6240.2421030.18822900.1923930.9620.9791000.187
6.624-9.3430.24940.218000.20218940.9640.9731000.207
9.343-89.4040.268470.30311000.30211510.9530.93999.65250.362

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