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- PDB-5o81: Crystal Structure of R67A/E173A Mutant of alpha-L-arabinofuranosi... -

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Basic information

Entry
Database: PDB / ID: 5o81
TitleCrystal Structure of R67A/E173A Mutant of alpha-L-arabinofuranosidase Ara51 from Clostridium thermocellum
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
Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)344,2326
Polymers344,2326
Non-polymers00
Water59433
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


Theoretical massNumber of molelcules
Total (without water)172,1163
Polymers172,1163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-18 kcal/mol
Surface area52700 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


Theoretical massNumber of molelcules
Total (without water)172,1163
Polymers172,1163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-15 kcal/mol
Surface area51780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.070, 173.070, 271.890
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 / Plasmid: p28LIC / Production host: Escherichia coli (E. coli)
References: UniProt: A3DIH0, non-reducing end alpha-L-arabinofuranosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.5→48.667 Å / Num. obs: 142438 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.279 % / Biso Wilson estimate: 52.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.104 / Χ2: 1.189 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.6513.1250.8612.94224050.6230.89698.6
2.65-2.8313.8130.624.34214800.8810.643100
2.83-3.0613.4910.3816.99199780.9670.396100
3.06-3.3513.5720.19713.94184520.9920.204100
3.35-3.7413.580.10825.29167590.9980.112100
3.74-4.3113.0610.06838.51148710.9990.071100
4.31-5.2712.7180.05249.44126650.9990.054100
5.27-7.4212.8330.04950.7199670.9990.051100
7.42-48.66711.9160.02969.55586110.03199.4

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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
PHENIXrefinement
XSCALEdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C7F

2c7f


Resolution: 2.5→48.667 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.16
RfactorNum. reflection% reflection
Rfree0.2408 7120 5 %
Rwork0.1933 --
obs0.1957 142408 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.53 Å2 / Biso mean: 57.4464 Å2 / Biso min: 27.88 Å2
Refinement stepCycle: final / Resolution: 2.5→48.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23710 0 0 33 23743
Biso mean---48.83 -
Num. residues----2975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124250
X-RAY DIFFRACTIONf_angle_d1.15432850
X-RAY DIFFRACTIONf_chiral_restr0.0653547
X-RAY DIFFRACTIONf_plane_restr0.0064249
X-RAY DIFFRACTIONf_dihedral_angle_d20.9598950
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 (%)
2.4976-2.5260.34152170.30774125434293
2.526-2.55570.35812360.292644854721100
2.5557-2.58680.33212350.291744624697100
2.5868-2.61960.3642350.285144774712100
2.6196-2.65410.33122350.269944584693100
2.6541-2.69040.31572360.266844804716100
2.6904-2.72880.29612330.255544344667100
2.7288-2.76960.29882360.244144794715100
2.7696-2.81280.30332350.253644744709100
2.8128-2.8590.33542360.264744884724100
2.859-2.90820.31362360.258744694705100
2.9082-2.96110.29832350.24644754710100
2.9611-3.01810.31212360.246444854721100
3.0181-3.07970.28892370.233544884725100
3.0797-3.14660.30552370.232645204757100
3.1466-3.21980.31722370.225844884725100
3.2198-3.30030.28792350.218244764711100
3.3003-3.38950.26792380.218445194757100
3.3895-3.48920.27582370.207744954732100
3.4892-3.60180.23962370.193645184755100
3.6018-3.73050.25872380.18945164754100
3.7305-3.87980.22432380.176245194757100
3.8798-4.05630.22032380.167145264764100
4.0563-4.270.20272390.154445334772100
4.27-4.53740.16872410.142445794820100
4.5374-4.88740.1872400.147445724812100
4.8874-5.37870.20342420.148945884830100
5.3787-6.15570.20822430.168846104853100
6.1557-7.75050.20232460.168746844930100
7.7505-48.67610.19682560.17694866512299

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