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- PDB-5ubj: Structure of an alpha-L-arabinofuranosidase (GH62) from Aspergill... -

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Basic information

Entry
Database: PDB / ID: 5ubj
TitleStructure of an alpha-L-arabinofuranosidase (GH62) from Aspergillus nidulans
ComponentsAlpha-L-arabinofuranosidase axhA-2
KeywordsHYDROLASE / arabinofuranosidase / hemicellulose
Function / homology
Function and homology information


arabinose metabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / pectin catabolic process / xylan catabolic process / extracellular region
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 axhA-2
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsLiberato, M.V. / Contesini, F.J. / Damasio, A.R. / Squina, F.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2014/50371-8 Brazil
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Structural and functional characterization of a highly secreted alpha-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse.
Authors: Contesini, F.J. / Liberato, M.V. / Rubio, M.V. / Calzado, F. / Zubieta, M.P. / Riano-Pachon, D.M. / Squina, F.M. / Bracht, F. / Skaf, M.S. / Damasio, A.R.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-L-arabinofuranosidase axhA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0616
Polymers35,8601
Non-polymers2005
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.562, 57.529, 49.371
Angle α, β, γ (deg.)90.000, 104.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-L-arabinofuranosidase axhA-2 / Arabinoxylan arabinofuranohydrolase axhA-2


Mass: 35860.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: axhA-2, AN7908 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5AUX2, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 1.63 Å3/Da / Density % sol: 24.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 32 % 2-Methyl-2,4-pentanediol, 10 % PEG8000, 0.1M calcium chloride, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.7→41.12 Å / Num. obs: 24535 / % possible obs: 96.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 14.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.036 / Rrim(I) all: 0.065 / Net I/σ(I): 14.7 / Num. measured all: 72250 / Scaling rejects: 53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.732.10.635250211770.6820.5340.8341.888.9
9-41.122.90.0365131780.9770.0260.04539.794.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4o8n

4o8n


Resolution: 1.7→28.764 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1777 1212 4.95 %
Rwork0.1441 23271 -
obs0.1458 24483 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.08 Å2 / Biso mean: 18.6386 Å2 / Biso min: 8.69 Å2
Refinement stepCycle: final / Resolution: 1.7→28.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 5 301 2620
Biso mean--22.11 28.98 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072412
X-RAY DIFFRACTIONf_angle_d0.9453315
X-RAY DIFFRACTIONf_chiral_restr0.055359
X-RAY DIFFRACTIONf_plane_restr0.006433
X-RAY DIFFRACTIONf_dihedral_angle_d3.2311883
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.76810.27851210.24712387250890
1.7681-1.84850.28511390.1982545268496
1.8485-1.9460.23581330.17362564269796
1.946-2.06790.20311280.15442573270196
2.0679-2.22750.19741390.14572606274597
2.2275-2.45150.18541440.14142631277598
2.4515-2.8060.18341200.14452643276398
2.806-3.53430.14551460.12692620276698
3.5343-28.76860.1351420.12162702284498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76050.15060.15491.34440.52410.97760.0089-0.0230.01810.0485-0.02520.06440.0183-0.0650.01740.12040.00540.01510.1444-0.00130.127741.3335-14.125715.6175
21.19990.0789-0.64520.54620.0751.96860.01060.054-0.0495-0.0746-0.04850.03570.0595-0.07890.04350.1313-0.006-0.0040.13970.00120.120541.9002-15.59952.8607
30.8848-0.1120.13391.2685-0.18671.77020.02220.04820.0416-0.0168-0.0199-0.1324-0.01370.1322-0.00140.10620.00250.01070.14680.00540.153159.7927-12.371410.7259
40.68240.05690.17891.03830.63221.33360.0305-0.10920.01780.1653-0.01460.03870.0129-0.0038-0.02220.11610.00750.00650.1339-0.00230.142446.0446-11.342720.3802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 78 )A23 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 145 )A79 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 264 )A146 - 264
4X-RAY DIFFRACTION4chain 'A' and (resid 265 through 325 )A265 - 325

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