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- PDB-1xnk: Beta-1,4-xylanase from Chaetomium thermophilum complexed with met... -

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Basic information

Entry
Database: PDB / ID: 1xnk
TitleBeta-1,4-xylanase from Chaetomium thermophilum complexed with methyl thioxylopentoside
Componentsendoxylanase 11A
KeywordsHYDROLASE / xylanase / glycoside hydrolase / family 11 / glycosidase / thioinhibitor / sulphur containing inhibitor
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
methyl pentopyranosyl-(1->4)-4-thiopentopyranosyl-(1->4)-4-thio-beta-D-xylopyranosyl-(1->4)-4-thio-beta-D-xylopyranosyl-(1->4)- 4-thio-alpha-D-xylopyranoside / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHakanpaa, J. / Hakulinen, N. / Rouvinen, J.
CitationJournal: FEBS J. / Year: 2005
Title: Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography
Authors: Janis, J. / Hakanpaa, J. / Hakulinen, N. / Ibatullin, F.M. / Hoxha, A. / Derrick, P.J. / Rouvinen, J. / Vainiotalo, P.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / 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 / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 14, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 3.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: endoxylanase 11A
B: endoxylanase 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2307
Polymers42,9882
Non-polymers1,2415
Water8,089449
1
A: endoxylanase 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0673
Polymers21,4941
Non-polymers5732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: endoxylanase 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1634
Polymers21,4941
Non-polymers6693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: endoxylanase 11A
B: endoxylanase 11A
hetero molecules

A: endoxylanase 11A
B: endoxylanase 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,45914
Polymers85,9764
Non-polymers2,48310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area5490 Å2
ΔGint-64 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.241, 57.593, 66.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1001-

SO4

21B-1000-

SO4

31A-1256-

HOH

41B-1184-

HOH

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Components

#1: Protein endoxylanase 11A


Mass: 21494.098 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Hypocrea jecorina (fungus) / References: UniProt: Q8J1V6, endo-1,4-beta-xylanase
#2: Polysaccharide 4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-methyl 4-thio-alpha-D-xylopyranoside


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 476.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: methyl pentopyranosyl-(1->4)-4-thiopentopyranosyl-(1->4)-4-thio-beta-D-xylopyranosyl-(1->4)-4-thio-beta-D-xylopyranosyl-(1->4)- 4-thio-alpha-D-xylopyranoside
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a212h-1a_1-5_1*OC][a212h-1b_1-5][a212h-1b_1-5_4*S]/1-2-3/a4-b1*S*_b4-c1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Xylp4SH]{[(4+S)][b-D-Xylp4SH]{[(4+S)][b-D-Xylp4SH]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 15, 2002 / Details: confocal optics by Osmic
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→99 Å / Num. all: 56502 / Num. obs: 56502 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.95 % / Biso Wilson estimate: 16.878 Å2 / Rsym value: 0.066 / Net I/σ(I): 11.7
Reflection shellResolution: 1.55→1.61 Å / Mean I/σ(I) obs: 1 / Num. unique all: 3124 / Rsym value: 0.296 / % possible all: 52.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H1A

1h1a


Resolution: 1.55→99 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 5744 -RANDOM
Rwork0.1974 ---
obs0.1974 56453 92.8 %-
all-56453 --
Displacement parametersBiso mean: 17.184 Å2
Refinement stepCycle: LAST / Resolution: 1.55→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 73 449 3510
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005322
X-RAY DIFFRACTIONc_angle_d1.5184

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