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- PDB-5o80: Crystal Structure of R67A Mutant of alpha-L-arabinofuranosidase A... -

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Basic information

Entry
Database: PDB / ID: 5o80
TitleCrystal Structure of R67A Mutant of alpha-L-arabinofuranosidase Ara51 from Clostridium thermocellum in complex with L-Arabinofuranose
ComponentsIntracellular exo-alpha-(1->5)-L-arabinofuranosidase
KeywordsHYDROLASE / Glycoside hydrolase / arabinofuranose / thioligase
Function / homology
Function and homology information


arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / cytoplasm
Similarity search - Function
Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-L-arabinofuranose / 1,4-DIETHYLENE DIOXIDE / Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.915 Å
AuthorsLafite, P. / Daniellou, R.
CitationJournal: To Be Published
Title: To be announced
Authors: Pennec, A. / Lafite, P. / Ferrieres, V. / Daniellou, R.
History
DepositionJun 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
B: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
C: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
D: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
E: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
F: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,00918
Polymers344,5806
Non-polymers1,42912
Water21612
1
A: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
C: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
D: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,0059
Polymers172,2903
Non-polymers7156
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-8 kcal/mol
Surface area52020 Å2
MethodPISA
2
B: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
E: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
F: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,0059
Polymers172,2903
Non-polymers7156
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-10 kcal/mol
Surface area51920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.740, 173.740, 271.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Intracellular exo-alpha-(1->5)-L-arabinofuranosidase / ABF / Intracellular arabinan exo-alpha-(1->5)-L-arabinosidase / Arabinosidase


Mass: 57429.969 Da / Num. of mol.: 6 / Mutation: R67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cthe_2548 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli)
References: UniProt: A3DIH0, non-reducing end alpha-L-arabinofuranosidase
#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.: 6
Source method: isolated from a genetically manipulated source
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-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1-4 dioxane, Na Cacodylate pH 6.5, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.91→48.76 Å / Num. obs: 90750 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.266 % / Biso Wilson estimate: 63.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.121 / Χ2: 1.039 / Net I/σ(I): 16.35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.91-3.0911.470.6163.87143340.9070.64599.2
3.09-3.311.1930.3356.87136060.9680.351100
3.3-3.5711.6110.20411.12127230.9870.214100
3.57-3.9111.2450.13416.22117080.9940.141100
3.91-4.3611.2350.09921.51106760.9960.104100
4.36-5.0311.5070.08326.494500.9970.087100
5.03-6.1411.080.08525.0980740.9960.089100
6.14-8.6210.90.07328.8663820.9970.077100
8.62-48.7610.160.0636.1437960.9980.06499.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.18 Å48.76 Å
Translation5.18 Å48.76 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASER2.5.2phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C7F

2c7f


Resolution: 2.915→48.76 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 24.57
RfactorNum. reflection% reflection
Rfree0.2464 4535 5 %
Rwork0.179 --
obs0.1824 90707 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 278.28 Å2 / Biso mean: 58.2049 Å2 / Biso min: 20.26 Å2
Refinement stepCycle: final / Resolution: 2.915→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23797 0 96 12 23905
Biso mean--61.41 46.21 -
Num. residues----2976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924487
X-RAY DIFFRACTIONf_angle_d1.18433165
X-RAY DIFFRACTIONf_chiral_restr0.0613582
X-RAY DIFFRACTIONf_plane_restr0.0074280
X-RAY DIFFRACTIONf_dihedral_angle_d3.59619447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9148-2.9480.36531450.28842751289696
2.948-2.98260.33041490.258928332982100
2.9826-3.0190.32061480.243728152963100
3.019-3.05720.33941500.2328452995100
3.0572-3.09740.31171500.23328513001100
3.0974-3.13990.30241480.225428222970100
3.1399-3.18470.32491500.218728352985100
3.1847-3.23220.31271500.226928462996100
3.2322-3.28270.28771490.21828392988100
3.2827-3.33650.30171490.214528362985100
3.3365-3.39410.31191500.202228442994100
3.3941-3.45580.27971500.195328553005100
3.4558-3.52220.28031500.19628563006100
3.5222-3.59410.29841500.196728422992100
3.5941-3.67220.28851510.187328693020100
3.6722-3.75760.25621500.168228462996100
3.7576-3.85150.21391510.170828793030100
3.8515-3.95560.24651500.165528503000100
3.9556-4.0720.22531510.16428543005100
4.072-4.20330.22551500.152828593009100
4.2033-4.35350.21741530.151529133066100
4.3535-4.52770.21411510.142328603011100
4.5277-4.73360.18221520.146928953047100
4.7336-4.98290.22561520.152728883040100
4.9829-5.29470.23881530.156728933046100
5.2947-5.7030.2211530.165829163069100
5.703-6.27580.24571540.176629243078100
6.2758-7.18150.23861560.1829603116100
7.1815-9.03850.17781570.148629883145100
9.0385-48.76680.22751630.19873108327199

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