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- PDB-5o82: Crystal Structure of R67A/E173A Mutant of alpha-L-arabinofuranosi... -

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Basic information

Entry
Database: PDB / ID: 5o82
TitleCrystal Structure of R67A/E173A Mutant of alpha-L-arabinofuranosidase Ara51 from Clostridium thermocellum in complex with 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 / Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.393 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)345,13212
Polymers344,2326
Non-polymers9016
Water4,666259
1
A: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
B: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
F: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,5666
Polymers172,1163
Non-polymers4503
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-20 kcal/mol
Surface area51520 Å2
MethodPISA
2
C: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
D: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
E: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,5666
Polymers172,1163
Non-polymers4503
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-23 kcal/mol
Surface area51850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.550, 170.550, 265.823
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: 57371.938 Da / Num. of mol.: 6 / Mutation: R67A E173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cthe_2548 / 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 natural 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.393→143.546 Å / Num. obs: 153754 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 45.91 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Rsym value: 0.086 / Net I/av σ(I): 6.6 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.393-2.5213.60.6521.20.1810.6770.65298.6
2.52-2.6813.40.4321.80.1220.4490.432100
2.68-2.8613.80.2652.90.0740.2750.265100
2.86-3.0913.60.1654.60.0460.1710.165100
3.09-3.3813.40.1017.20.0290.1060.101100
3.38-3.7813.60.0759.20.0210.0780.075100
3.78-4.3713.20.06110.60.0170.0640.061100
4.37-5.3512.90.05611.10.0160.0580.056100
5.35-7.5712.80.05511.50.0160.0580.055100
7.57-48.647120.04611.30.0140.0480.04699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.97 Å48.67 Å
Translation8.97 Å48.67 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
SCALA3.3.2data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C7F

2c7f


Resolution: 2.393→47.849 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.86
RfactorNum. reflection% reflection
Rfree0.2367 7710 5.02 %
Rwork0.1871 --
obs0.1895 153608 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.4 Å2 / Biso mean: 50.7215 Å2 / Biso min: 23.82 Å2
Refinement stepCycle: final / Resolution: 2.393→47.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23751 0 60 259 24070
Biso mean--45.47 38.64 -
Num. residues----2973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924367
X-RAY DIFFRACTIONf_angle_d1.0733011
X-RAY DIFFRACTIONf_chiral_restr0.063575
X-RAY DIFFRACTIONf_plane_restr0.0064258
X-RAY DIFFRACTIONf_dihedral_angle_d3.65215499
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 (%)
2.3927-2.41990.30882250.24034501472694
2.4199-2.44840.28562640.235748235087100
2.4484-2.47830.29482650.234748025067100
2.4783-2.50960.3252620.239548355097100
2.5096-2.54270.31072460.236148005046100
2.5427-2.57750.31482370.23648235060100
2.5775-2.61430.32432350.248248455080100
2.6143-2.65330.32812670.247448135080100
2.6533-2.69480.28072690.228348085077100
2.6948-2.7390.29112640.228448165080100
2.739-2.78620.2962710.226348035074100
2.7862-2.83680.2722650.22448275092100
2.8368-2.89140.30882780.232848515129100
2.8914-2.95040.27242450.23548295074100
2.9504-3.01450.27822760.232748155091100
3.0145-3.08470.28532560.22548405096100
3.0847-3.16180.28792440.21948705114100
3.1618-3.24730.26232490.209248415090100
3.2473-3.34280.26762210.203249305151100
3.3428-3.45070.23832540.194648555109100
3.4507-3.57390.25382290.192749045133100
3.5739-3.7170.22062570.17948915148100
3.717-3.88610.22752860.164148485134100
3.8861-4.09090.21062750.159348785153100
4.0909-4.3470.18222430.146749185161100
4.347-4.68240.18342610.142149075168100
4.6824-5.15310.17642730.146349725245100
5.1531-5.89760.20732500.158449915241100
5.8976-7.42590.21172700.176150285298100
7.4259-47.85810.21332730.17755234550799

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