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- PDB-2bnj: The xylanase TA from Thermoascus aurantiacus utilizes arabinose d... -

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Basic information

Entry
Database: PDB / ID: 2bnj
TitleThe xylanase TA from Thermoascus aurantiacus utilizes arabinose decorations of xylan as significant substrate specificity determinants.
ComponentsENDO-1,4-BETA-XYLANASEXylanase
KeywordsHYDROLASE / XYLANASE / GLYCOSIDASE / PYRROLIDONE CARBOXYLIC ACID / XYLAN DEGRADATION
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesTHERMOASCUS AURANTIACUS (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVardakou, M. / Murray, J.W. / Flint, J. / Christakopoulos, P. / Lewis, R.J. / Gilbert, H.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: A Family 10 Thermoascus Aurantiacus Xylanase Utilizes Arabinose Decorations of Xylan as Significant Substrate Specificity Determinants.
Authors: Vardakou, M. / Flint, J. / Christakopoulos, P. / Lewis, R.J. / Gilbert, H.J. / Murray, J.W.
History
DepositionMar 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 13, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4573
Polymers32,8491
Non-polymers6092
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.224, 49.462, 77.384
Angle α, β, γ (deg.)90.00, 125.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2295-

HOH

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE / Xylanase / FAMILY 10 XYLANASE / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE / TAXI


Mass: 32848.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMOASCUS AURANTIACUS (fungus) / Variant: MIECHE, IMI 216529 / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Polysaccharide alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-3DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a212h-1b_1-5][a211h-1a_1-4]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][a-L-5-deoxy-Araf]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID / Ferulic acid


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS

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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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growDetails: 13.5% PEG 6K, 2.5MM FAX2, 4MG/ML TA PROTEIN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20.45 Å / Num. obs: 34409 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 2.64 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 25.12
Reflection shellResolution: 1.6→1.61 Å / Redundancy: 2.44 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 9.31 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I1X

1i1x


Resolution: 1.6→63.12 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.097 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.147 1689 4.99 %RANDOM
Rwork0.115 ---
obs0.117 34409 95.4 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.095 Å20 Å20.005 Å2
2---0.037 Å20 Å2
3----0.053 Å2
Refinement stepCycle: LAST / Resolution: 1.6→63.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 41 596 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9483313
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51925.37108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51315364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3621510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022724
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.2513
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21231
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2422
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.26
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7741.51941
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97922440
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8931082
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4734.5870
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 7.11→63.12 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.144 17
Rwork0.132 392

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