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- PDB-4n4b: Crystal Structure of the alpha-L-arabinofuranosidase PaAbf62A fro... -

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Basic information

Entry
Database: PDB / ID: 4n4b
TitleCrystal Structure of the alpha-L-arabinofuranosidase PaAbf62A from Podospora anserina
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-L-arabinofuranosidase
Similarity search - Component
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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)40,8375
Polymers40,1981
Non-polymers6394
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.410, 66.830, 60.570
Angle α, β, γ (deg.)90.00, 117.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-404-

1PE

21A-1176-

HOH

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Components

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Protein , 1 types, 1 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

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Non-polymers , 5 types, 419 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.44→45 Å / Num. all: 65750 / Num. obs: 60688 / % possible obs: 92.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.56 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 21.86
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 2 % / Mean I/σ(I) obs: 8.26 / Num. unique all: 3880 / Rsym value: 0.093 / % possible all: 80.3

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Processing

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

4n1i


Resolution: 1.44→44.61 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.709 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15192 3039 5 %RANDOM
Rwork0.12812 ---
obs0.12931 57650 92.51 %-
all-65231 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.643 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.05 Å2
2---0.11 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.44→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 37 415 2974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022707
X-RAY DIFFRACTIONr_bond_other_d0.0010.022409
X-RAY DIFFRACTIONr_angle_refined_deg2.5211.9273715
X-RAY DIFFRACTIONr_angle_other_deg1.0163.0015550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6695338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77224.559136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33315382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6861512
X-RAY DIFFRACTIONr_chiral_restr0.1450.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213169
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02677
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_it1.6971.2161299
X-RAY DIFFRACTIONr_mcbond_other1.6821.2131297
X-RAY DIFFRACTIONr_mcangle_it2.581.8261627
X-RAY DIFFRACTIONr_mcangle_other2.5821.8281628
X-RAY DIFFRACTIONr_scbond_it2.8231.4281408
X-RAY DIFFRACTIONr_scbond_other2.8231.4281408
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0642.0532080
X-RAY DIFFRACTIONr_long_range_B_refined6.20111.93459
X-RAY DIFFRACTIONr_long_range_B_other5.86610.9843233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 202 -
Rwork0.162 3668 -
obs--80.39 %

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