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- PDB-9fnl: The structure of CBM42 from Clostridium thermocellum in complex w... -

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Basic information

Entry
Database: PDB / ID: 9fnl
TitleThe structure of CBM42 from Clostridium thermocellum in complex with arabinofuranosyl xylobiose (A3X) substrate molecules
ComponentsAnti-sigma-I factor RsgI5
KeywordsSUGAR BINDING PROTEIN / CBM42 / Clostridium thermocellum
Function / homology
Function and homology information


L-arabinose metabolic process / alpha-L-arabinofuranosidase activity / plasma membrane
Similarity search - Function
: / Anti-sigma factor RsgI-like central domain / Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain
Similarity search - Domain/homology
Anti-sigma-I factor RsgI5
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHadad, N. / Lavid, N. / Shoham, Y. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of CBM42 from Clostridium thermocellum in complex with arabinofuranosyl xylobiose (A3X) substrate molecules
Authors: Hadad, N. / Lavid, N. / Shoham, Y. / Shoham, G.
History
DepositionJun 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 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: Anti-sigma-I factor RsgI5
B: Anti-sigma-I factor RsgI5
C: Anti-sigma-I factor RsgI5
D: Anti-sigma-I factor RsgI5
E: Anti-sigma-I factor RsgI5
F: Anti-sigma-I factor RsgI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,73234
Polymers97,1366
Non-polymers5,59628
Water16,736929
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14350 Å2
ΔGint-147 kcal/mol
Surface area39030 Å2
Unit cell
Length a, b, c (Å)55.169, 76.283, 77.766
Angle α, β, γ (deg.)91.115, 110.658, 99.461
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Anti-sigma-I factor RsgI5


Mass: 16189.264 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: rsgI5, Cthe_1273 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DEX6
#2: Polysaccharide
alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 12 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-3DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a212h-1b_1-5][a211h-1a_1-4]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][a-L-Araf]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0M Ammonium sulfate and 0.1M MES buffer at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→35.93 Å / Num. obs: 66427 / % possible obs: 97.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 27.37 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.064 / Rrim(I) all: 0.1 / Net I/σ(I): 5.3
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4460 / CC1/2: 0.87 / Rpim(I) all: 0.22 / Rrim(I) all: 0.37

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.93 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.4861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 3166 4.77 %
Rwork0.1641 63224 -
obs0.1664 66390 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7158 0 15 929 8102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717379
X-RAY DIFFRACTIONf_angle_d0.976710001
X-RAY DIFFRACTIONf_chiral_restr0.05811092
X-RAY DIFFRACTIONf_plane_restr0.0051218
X-RAY DIFFRACTIONf_dihedral_angle_d13.35961202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.25981150.21172733X-RAY DIFFRACTION97.04
2.13-2.160.21861270.19642765X-RAY DIFFRACTION96.11
2.16-2.20.24391270.19082777X-RAY DIFFRACTION97.45
2.2-2.240.25191460.19422680X-RAY DIFFRACTION97.05
2.24-2.280.27541470.1962730X-RAY DIFFRACTION97.46
2.28-2.320.24711360.19422734X-RAY DIFFRACTION97.42
2.32-2.370.24771510.1842746X-RAY DIFFRACTION97.08
2.37-2.420.24671480.18682753X-RAY DIFFRACTION97.78
2.42-2.480.22641280.17872735X-RAY DIFFRACTION97.41
2.48-2.540.27271300.1822757X-RAY DIFFRACTION97.53
2.54-2.610.23481490.18822770X-RAY DIFFRACTION97.63
2.61-2.690.26611310.18462702X-RAY DIFFRACTION95.55
2.69-2.770.28051340.19232746X-RAY DIFFRACTION97.79
2.77-2.870.24091440.19522746X-RAY DIFFRACTION98.17
2.87-2.990.23951370.1782795X-RAY DIFFRACTION98.39
2.99-3.120.22161430.17192730X-RAY DIFFRACTION98.46
3.12-3.290.22971680.16882752X-RAY DIFFRACTION98.42
3.29-3.490.21741420.16082776X-RAY DIFFRACTION98.12
3.49-3.760.17841310.14332724X-RAY DIFFRACTION96.65
3.76-4.140.15031360.13532750X-RAY DIFFRACTION97.57
4.14-4.740.17811220.11872801X-RAY DIFFRACTION99.12
4.74-5.960.16491220.13272821X-RAY DIFFRACTION98.92
5.96-35.930.17411520.17432701X-RAY DIFFRACTION96.52

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