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- PDB-5la1: The mechanism by which arabinoxylanases can recognise highly deco... -

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Basic information

Entry
Database: PDB / ID: 5la1
TitleThe mechanism by which arabinoxylanases can recognise highly decorated xylans
ComponentsCarbohydrate binding family 6
KeywordsHYDROLASE / Arabinoxylanase Glycoside hydrolase Carbohydrate binding module Arabinose Clostridium thermocellum Cellulosome
Function / homology
Function and homology information


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / metal ion binding
Similarity search - Function
Ricin-type beta-trefoil lectin domain-like / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. ...Ricin-type beta-trefoil lectin domain-like / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Ricin B, lectin domain / Ricin B-like lectins / Galactose-binding domain-like / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / beta-D-xylopyranose / : / Carbohydrate binding family 6
Similarity search - Component
Biological speciesRuminiclostridium thermocellum JW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBasle, A. / Labourel, A. / Cuskin, F. / Jackson, A. / Crouch, L. / Rogowski, A. / Gilbert, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K020358/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans.
Authors: Labourel, A. / Crouch, L.I. / Bras, J.L. / Jackson, A. / Rogowski, A. / Gray, J. / Yadav, M.P. / Henrissat, B. / Fontes, C.M. / Gilbert, H.J. / Najmudin, S. / Basle, A. / Cuskin, F.
History
DepositionJun 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Oct 24, 2018Group: 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_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
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_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate binding family 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9459
Polymers54,1581
Non-polymers7878
Water10,791599
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-16 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.911, 72.514, 109.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbohydrate binding family 6


Mass: 54157.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum JW20 (bacteria)
Gene: Cther_1146 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J9WZQ7, UniProt: A3DHG6*PLUS
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 100 mM Na/K phosphate, 100 mM MES pH 6.5 and 2M NaCl.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.9→45.16 Å / Num. obs: 42716 / % possible obs: 98.6 % / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Net I/σ(I): 26.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 8 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AK1

5ak1
PDB Unreleased entry


Resolution: 1.9→45.16 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.073 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16041 2090 4.9 %RANDOM
Rwork0.12944 ---
obs0.13097 40566 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.065 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 47 599 4350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023890
X-RAY DIFFRACTIONr_bond_other_d0.0020.023503
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9385316
X-RAY DIFFRACTIONr_angle_other_deg0.99238039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87823.684190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45215550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3251526
X-RAY DIFFRACTIONr_chiral_restr0.2220.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02962
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_it1.0871.4811906
X-RAY DIFFRACTIONr_mcbond_other1.0721.4791905
X-RAY DIFFRACTIONr_mcangle_it1.6432.2122382
X-RAY DIFFRACTIONr_mcangle_other1.6462.2132383
X-RAY DIFFRACTIONr_scbond_it1.6391.6611984
X-RAY DIFFRACTIONr_scbond_other1.6391.6611984
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5872.4272929
X-RAY DIFFRACTIONr_long_range_B_refined5.72220.9745073
X-RAY DIFFRACTIONr_long_range_B_other5.72220.9795074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 125 -
Rwork0.142 2605 -
obs--86.12 %

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