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- PDB-1qw9: Crystal structure of a family 51 alpha-L-arabinofuranosidase in c... -

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Basic information

Entry
Database: PDB / ID: 1qw9
TitleCrystal structure of a family 51 alpha-L-arabinofuranosidase in complex with 4-nitrophenyl-Ara
ComponentsAlpha-L-arabinofuranosidase
KeywordsHYDROLASE
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
4-nitrophenyl alpha-L-arabinofuranoside / Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHoevel, K. / Shallom, D. / Niefind, K. / Belakhov, V. / Shoham, G. / Bassov, 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
DepositionSep 1, 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: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,9964
Polymers114,4542
Non-polymers5422
Water28,6081588
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)344,98912
Polymers343,3616
Non-polymers1,6276
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)179.311, 179.311, 100.397
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2425-

HOH

21B-2422-

HOH

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Components

#1: Protein Alpha-L-arabinofuranosidase / Arabinosidase


Mass: 57226.863 Da / Num. of mol.: 2 / Mutation: E175A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: ABFA / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9XBQ3, non-reducing end alpha-L-arabinofuranosidase
#2: Sugar ChemComp-KHP / 4-nitrophenyl alpha-L-arabinofuranoside / 2-HYDROXYMETHYL-5-(4-NITRO-PHENOXY)-TETRAHYDRO-FURAN-3,4-DIOL / 4-NITROPHENYL-ARA / 4-nitrophenyl alpha-L-arabinoside / 4-nitrophenyl L-arabinoside / 4-nitrophenyl arabinoside


Type: L-saccharide / Mass: 271.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13NO7
IdentifierTypeProgram
4-nitrophenyl-AraIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1588 / 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: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18 % PEG 3350, 0.2 M NH4F, 5 % 2-propanol, 0.1 M Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8459 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 370234 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.2→1.24 Å / % possible all: 97.9
Reflection
*PLUS
Num. obs: 370260 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.179 17580 5 %random
Rwork0.16 ---
obs0.173 351590 98.84 %-
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7972 0 38 1588 9598
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1563

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