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- PDB-3s2c: Structure of the thermostable GH51 alpha-L-arabinofuranosidase fr... -

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Basic information

Entry
Database: PDB / ID: 3s2c
TitleStructure of the thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1
ComponentsAlpha-N-arabinofuranosidase
KeywordsHYDROLASE / TIM-barrel and jelly-roll domains / alpha-L-arabinofuranosidase / glycosyl hydrolase 51 family
Function / homology
Function and homology information


L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity
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-N-arabinofuranosidase
Similarity search - Component
Biological speciesThermotoga petrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSouza, T.A.C.B. / Santos, C.R. / Souza, A.R. / Oldiges, D.P. / Ruller, R. / Prade, R.A. / Squina, F.M. / Murakami, M.T.
CitationJournal: Protein Sci. / Year: 2011
Title: Structure of a novel thermostable GH51 Alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1
Authors: Souza, T.A. / Santos, C.R. / Souza, A.R. / Oldiges, D.P. / Ruller, R. / Prade, R.A. / Squina, F.M. / Murakami, M.T.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-N-arabinofuranosidase
B: Alpha-N-arabinofuranosidase
C: Alpha-N-arabinofuranosidase
D: Alpha-N-arabinofuranosidase
E: Alpha-N-arabinofuranosidase
F: Alpha-N-arabinofuranosidase
G: Alpha-N-arabinofuranosidase
H: Alpha-N-arabinofuranosidase
I: Alpha-N-arabinofuranosidase
J: Alpha-N-arabinofuranosidase
K: Alpha-N-arabinofuranosidase
L: Alpha-N-arabinofuranosidase


Theoretical massNumber of molelcules
Total (without water)664,18412
Polymers664,18412
Non-polymers00
Water7,800433
1
A: Alpha-N-arabinofuranosidase
B: Alpha-N-arabinofuranosidase
C: Alpha-N-arabinofuranosidase
D: Alpha-N-arabinofuranosidase
E: Alpha-N-arabinofuranosidase
F: Alpha-N-arabinofuranosidase


Theoretical massNumber of molelcules
Total (without water)332,0926
Polymers332,0926
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-48 kcal/mol
Surface area99150 Å2
MethodPISA
2
G: Alpha-N-arabinofuranosidase
H: Alpha-N-arabinofuranosidase
I: Alpha-N-arabinofuranosidase
J: Alpha-N-arabinofuranosidase
K: Alpha-N-arabinofuranosidase
L: Alpha-N-arabinofuranosidase


Theoretical massNumber of molelcules
Total (without water)332,0926
Polymers332,0926
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-47 kcal/mol
Surface area100520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.950, 187.292, 180.636
Angle α, β, γ (deg.)90.00, 90.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-N-arabinofuranosidase


Mass: 55348.707 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga petrophila (bacteria) / Strain: RKU-1 / Gene: Tpet_0631 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) SlyD
References: UniProt: A5IKC8, non-reducing end alpha-L-arabinofuranosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2010
RadiationMonochromator: double-crystal - Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 137481 / Num. obs: 137481 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 97

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PZ3

1pz3


Resolution: 3→49.24 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.863 / SU B: 19.831 / SU ML: 0.369 / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 6914 5 %RANDOM
Rwork0.195 ---
obs0.198 130569 97.17 %-
all-137481 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.462 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.19 Å2
2--0.09 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 3→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46699 0 0 433 47132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02247885
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9564966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09155786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47324.2432317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.66158185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7615265
X-RAY DIFFRACTIONr_chiral_restr0.1030.27007
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02136629
X-RAY DIFFRACTIONr_mcbond_it0.4211.528790
X-RAY DIFFRACTIONr_mcangle_it0.829246687
X-RAY DIFFRACTIONr_scbond_it1.147319095
X-RAY DIFFRACTIONr_scangle_it2.0354.518279
LS refinement shellResolution: 3→3.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 468 -
Rwork0.3 8655 -
obs--87.41 %

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