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- PDB-4n2z: Crystal Structure of the alpha-L-arabinofuranosidase PaAbf62A fro... -

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Basic information

Entry
Database: PDB / ID: 4n2z
TitleCrystal Structure of the alpha-L-arabinofuranosidase PaAbf62A from Podospora anserina in complex with cellotriose
ComponentsGH62 arabinofuranosidase
KeywordsHYDROLASE / Beta-Propeller / hemicellulose binding
Function / homology
Function and homology information


L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / extracellular region / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 62, arabinosidase / Glycosyl hydrolase family 62 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
alpha-cellotriose / Alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSiguier, B. / Dumon, C. / Mourey, L. / Tranier, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: First Structural Insights into alpha-L-Arabinofuranosidases from the Two GH62 Glycoside Hydrolase Subfamilies.
Authors: Siguier, B. / Haon, M. / Nahoum, V. / Marcellin, M. / Burlet-Schiltz, O. / Coutinho, P.M. / Henrissat, B. / Mourey, L. / O'Donohue, M.J. / Berrin, J.G. / Tranier, S. / Dumon, C.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: 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
Revision 2.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH62 arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3426
Polymers40,1981
Non-polymers1,1435
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.140, 66.790, 60.360
Angle α, β, γ (deg.)90.00, 117.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1265-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein GH62 arabinofuranosidase / alpha-L-arabinofuranosidase PaAbf62A


Mass: 40198.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Strain: S Mat+ / Production host: Pichia pastoris (fungus)
References: UniProt: E2GHW5, non-reducing end alpha-L-arabinofuranosidase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 374 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 4000, 0.2M Calcium chloride, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: Nova high-flux-micro-focus sealed tube / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Oct 2, 2011
RadiationMonochromator: multi-layer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 32914 / Num. obs: 32128 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.071 / Net I/σ(I): 22
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.51 / Num. unique all: 2414 / Rsym value: 0.381 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N1I

4n1i


Resolution: 1.8→14.84 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.793 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.094 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16963 1687 5.1 %RANDOM
Rwork0.13113 ---
obs0.13309 31660 99.58 %-
all-31794 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.937 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→14.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 71 370 2955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022735
X-RAY DIFFRACTIONr_bond_other_d0.0010.022432
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.9443758
X-RAY DIFFRACTIONr_angle_other_deg0.9363.0015618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7915339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09424.667135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.715385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5831511
X-RAY DIFFRACTIONr_chiral_restr0.1250.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.361.0991294
X-RAY DIFFRACTIONr_mcbond_other1.3251.0961292
X-RAY DIFFRACTIONr_mcangle_it2.1331.6431620
X-RAY DIFFRACTIONr_mcangle_other2.1351.6461621
X-RAY DIFFRACTIONr_scbond_it2.2251.3061441
X-RAY DIFFRACTIONr_scbond_other2.2261.3061441
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.31.8932128
X-RAY DIFFRACTIONr_long_range_B_refined5.50710.2973458
X-RAY DIFFRACTIONr_long_range_B_other5.50810.3063459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 134 -
Rwork0.188 2208 -
obs--97.3 %

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