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- PDB-9nxj: The GH43 domain of an alpha-l-arabinofuranosidase (AtAbf43C_GH43)... -

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Basic information

Entry
Database: PDB / ID: 9nxj
TitleThe GH43 domain of an alpha-l-arabinofuranosidase (AtAbf43C_GH43) from Acetivibrio thermocellus DSM1313
ComponentsGlycoside hydrolase family 43
KeywordsHYDROLASE / FIVE-BLADED BETA PROPELLER / BETA-TREFOIL / FUROSIDASE
Function / homology
Function and homology information


L-arabinose metabolic process / alpha-L-arabinofuranosidase activity / polysaccharide catabolic process
Similarity search - Function
Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat ...Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily
Similarity search - Domain/homology
alpha-L-arabinofuranose / Glycoside hydrolase family 43
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsGalindo, J.L. / Jeffrey, P.D. / Conway, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateEnergy Research Fund administered by the Andlinger Center for Energy and the Environment at Princeton University United States
CitationJournal: Biochem.J. / Year: 2025
Title: Functional and structural characterization of AtAbf43C: an exo-1,5-alpha-L-arabinofuranosidase from Acetivibrio thermocellus DSM1313.
Authors: Galindo, J.L. / Jeffrey, P.D. / Zhu, A. / Link, A.J. / Conway, J.M.
History
DepositionMar 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 43
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8918
Polymers76,2072
Non-polymers6856
Water1,58588
1
A: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5425
Polymers38,1031
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3503
Polymers38,1031
Non-polymers2462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.304, 105.304, 128.856
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVAL(chain 'A' and (resid 149 through 163 or resid 165...AA149 - 1633 - 17
12ARGARGILEILE(chain 'A' and (resid 149 through 163 or resid 165...AA165 - 33819 - 192
13ALAALAPROPRO(chain 'A' and (resid 149 through 163 or resid 165...AA341 - 474195 - 328
14AHRAHRAHRAHR(chain 'A' and (resid 149 through 163 or resid 165...AC501
25PROPROVALVAL(chain 'B' and (resid 149 through 163 or resid 165...BB149 - 1633 - 17
26ARGARGILEILE(chain 'B' and (resid 149 through 163 or resid 165...BB164 - 33818 - 192
27ALAALAPROPRO(chain 'B' and (resid 149 through 163 or resid 165...BB341 - 473195 - 327
28AHRAHRAHRAHR(chain 'B' and (resid 149 through 163 or resid 165...BG501

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Components

#1: Protein Glycoside hydrolase family 43


Mass: 38103.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: Cthe_2138 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DHB3
#2: Sugar ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEGmme 5000, pH 5.5 Bis-Tris, AmS04

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92015 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92015 Å / Relative weight: 1
ReflectionResolution: 2.32→29.59 Å / Num. obs: 35192 / % possible obs: 99.7 % / Redundancy: 20.6 % / Biso Wilson estimate: 41.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.027 / Rrim(I) all: 0.121 / Χ2: 0.98 / Net I/σ(I): 21.2 / Num. measured all: 724982
Reflection shellResolution: 2.32→2.38 Å / % possible obs: 96.1 % / Redundancy: 20.2 % / Rmerge(I) obs: 0.852 / Num. measured all: 50475 / Num. unique obs: 2503 / CC1/2: 0.867 / Rpim(I) all: 0.192 / Rrim(I) all: 0.874 / Χ2: 0.54 / Net I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→29.59 Å / SU ML: 0.3461 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.8714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1644 4.76 %
Rwork0.2027 32864 -
obs0.2049 34508 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.99 Å2
Refinement stepCycle: LAST / Resolution: 2.32→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5192 0 40 88 5320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085408
X-RAY DIFFRACTIONf_angle_d0.99187396
X-RAY DIFFRACTIONf_chiral_restr0.0609788
X-RAY DIFFRACTIONf_plane_restr0.007950
X-RAY DIFFRACTIONf_dihedral_angle_d18.83211943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.36661470.29152578X-RAY DIFFRACTION93.29
2.38-2.460.35951100.27392692X-RAY DIFFRACTION96.02
2.46-2.550.35021550.26952706X-RAY DIFFRACTION97.05
2.55-2.650.35631300.25422712X-RAY DIFFRACTION97.4
2.65-2.770.31351350.25432724X-RAY DIFFRACTION97.08
2.77-2.920.30661310.24752691X-RAY DIFFRACTION97.18
2.92-3.10.27171570.24042761X-RAY DIFFRACTION98.65
3.1-3.340.31471140.23352779X-RAY DIFFRACTION99.31
3.34-3.670.2631290.21242797X-RAY DIFFRACTION99.59
3.67-4.20.22151560.18032791X-RAY DIFFRACTION99.7
4.2-5.290.17591420.14642797X-RAY DIFFRACTION99.8
5.29-29.590.18311380.16372836X-RAY DIFFRACTION99.77

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