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- PDB-1pz3: Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosida... -

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Basic information

Entry
Database: PDB / ID: 1pz3
TitleCrystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6
ComponentsAlpha-L-arabinofuranosidase
KeywordsHYDROLASE / beta-alpha8-barrel
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 speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHoevel, K. / Shallom, D. / Niefind, K. / Belakhov, V. / Shoham, G. / Baasov, T. / Shoham, Y. / Schomburg, D.
CitationJournal: Embo J. / Year: 2003
Title: Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase
Authors: Hoevel, K. / Shallom, D. / Niefind, K. / Belakhov, V. / Shoham, G. / Baasov, T. / Shoham, Y. / Schomburg, D.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-L-arabinofuranosidase
B: Alpha-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7544
Polymers114,5702
Non-polymers1842
Water20,6091144
1
A: Alpha-L-arabinofuranosidase
B: Alpha-L-arabinofuranosidase
hetero molecules

A: Alpha-L-arabinofuranosidase
B: Alpha-L-arabinofuranosidase
hetero molecules

A: Alpha-L-arabinofuranosidase
B: Alpha-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,26212
Polymers343,7096
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)179.430, 179.430, 100.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Alpha-L-arabinofuranosidase / Arabinosidase


Mass: 57284.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: T-6 / Gene: ABFA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9XBQ3, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1144 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18 % PEG 3350, 0.2 M NH4F, 100 mM Tris/HCl, 5% 2-Propanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
123 %(w/v)PEG33501reservoir
20.2 M1reservoirNH4F
35 %(v/v)2-propanol1reservoir
40.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 9, 2002 / Details: osmic mirror
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 120071 / Num. obs: 119711 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.75→1.79 Å / % possible all: 99.7
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.204 5985 RANDOM
Rwork0.171 --
all-120071 -
obs-119711 -
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7980 0 12 1144 9136
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1490

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