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- PDB-6q8n: GH10 endo-xylanase in complex with xylobiose epoxide inhibitor -

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Basic information

Entry
Database: PDB / ID: 6q8n
TitleGH10 endo-xylanase in complex with xylobiose epoxide inhibitor
ComponentsBeta-xylanase
KeywordsHYDROLASE
Function / homology
Function and homology information


cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 ...CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / 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
Chem-HQ8 / : / beta-D-xylopyranose / Beta-xylanase
Similarity search - Component
Biological speciesAspergillus aculeatus ATCC 16872 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDavies, G.J. / Rowland, R.J. / Wu, L. / Moroz, O. / Blagova, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
CitationJournal: Acs Cent.Sci. / Year: 2019
Title: Dynamic and Functional Profiling of Xylan-Degrading Enzymes inAspergillusSecretomes Using Activity-Based Probes.
Authors: Schroder, S.P. / de Boer, C. / McGregor, N.G.S. / Rowland, R.J. / Moroz, O. / Blagova, E. / Reijngoud, J. / Arentshorst, M. / Osborn, D. / Morant, M.D. / Abbate, E. / Stringer, M.A. / Krogh, ...Authors: Schroder, S.P. / de Boer, C. / McGregor, N.G.S. / Rowland, R.J. / Moroz, O. / Blagova, E. / Reijngoud, J. / Arentshorst, M. / Osborn, D. / Morant, M.D. / Abbate, E. / Stringer, M.A. / Krogh, K.B.R.M. / Raich, L. / Rovira, C. / Berrin, J.G. / van Wezel, G.P. / Ram, A.F.J. / Florea, B.I. / van der Marel, G.A. / Codee, J.D.C. / Wilson, K.S. / Wu, L. / Davies, G.J. / Overkleeft, H.S.
History
DepositionDec 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 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_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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 2.1Jan 24, 2024Group: 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,01738
Polymers85,8112
Non-polymers3,20536
Water11,367631
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,57020
Polymers42,9061
Non-polymers1,66519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,44618
Polymers42,9061
Non-polymers1,54117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.120, 75.750, 221.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-xylanase


Mass: 42905.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus ATCC 16872 (mold)
Gene: ASPACDRAFT_127619 / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A1L9WG58, endo-1,4-beta-xylanase

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Sugars , 2 types, 6 molecules

#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 661 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-HQ8 / (1~{R},2~{S},4~{S},5~{R})-cyclohexane-1,2,3,4,5-pentol


Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Sodium/potassium phosphate (pH 6.9). Co-crystallisation with xylobiose epoxide inhibitor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.76→62.57 Å / Num. obs: 81568 / % possible obs: 99.96 % / Redundancy: 7.95 % / Rpim(I) all: 0.044 / Net I/σ(I): 10.69
Reflection shellResolution: 1.76→1.79 Å / Mean I/σ(I) obs: 1.07 / Num. unique obs: 4016 / Rpim(I) all: 0.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7B

3u7b


Resolution: 1.76→62.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.601 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20473 4031 4.9 %RANDOM
Rwork0.16699 ---
obs0.16886 77449 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.914 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0 Å20 Å2
2--0.15 Å2-0 Å2
3----1.76 Å2
Refinement stepCycle: 1 / Resolution: 1.76→62.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 200 631 5692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135221
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174632
X-RAY DIFFRACTIONr_angle_refined_deg1.751.6757129
X-RAY DIFFRACTIONr_angle_other_deg1.4411.59110755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6595654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40924.795219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10815718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.604158
X-RAY DIFFRACTIONr_chiral_restr0.090.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025831
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021045
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_it1.8682.512601
X-RAY DIFFRACTIONr_mcbond_other1.8682.5092600
X-RAY DIFFRACTIONr_mcangle_it2.3613.7483260
X-RAY DIFFRACTIONr_mcangle_other2.363.753261
X-RAY DIFFRACTIONr_scbond_it2.3912.692620
X-RAY DIFFRACTIONr_scbond_other2.392.692621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2563.9343870
X-RAY DIFFRACTIONr_long_range_B_refined4.37330.5265770
X-RAY DIFFRACTIONr_long_range_B_other4.37230.5265771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 302 -
Rwork0.352 5633 -
obs--99.88 %

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