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- PDB-5la2: The mechanism by which arabinoxylanases can recognise highly deco... -

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Basic information

Entry
Database: PDB / ID: 5la2
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
beta-L-arabinopyranose / : / Carbohydrate binding family 6
Similarity search - Component
Biological speciesRuminiclostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate binding family 6
B: Carbohydrate binding family 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,12912
Polymers108,2312
Non-polymers1,89810
Water16,628923
1
A: Carbohydrate binding family 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0656
Polymers54,1161
Non-polymers9495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbohydrate binding family 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0656
Polymers54,1161
Non-polymers9495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.273, 123.176, 125.380
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 / GH5-CBM6


Mass: 54115.652 Da / Num. of mol.: 2 / Fragment: UNP residues 37-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum (bacteria)
Gene: Cther_1146 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J9WZQ7, UniProt: A3DHG6*PLUS
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-L- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-L-arabinofuranose-(1-3)]alpha-D-xylopyranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4[LArafa1-3]DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a212h-1a_1-5][a211h-1a_1-4][a212h-1b_1-5]/1-2-3-3-3/a3-b1_a4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(3+1)][a-L-Araf]{}[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-ARB / beta-L-arabinopyranose / beta-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinopyranoseCOMMON NAMEGMML 1.0
b-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 100 mM Tris-Bicine buffer pH 8.5, 12.5% (w/v) polyethylene glycol average Mw 1,000 Da, 12.5% (w/v) polyethylene glycol average Mw 3,350 Da and 12.5% (RS)-2-methyl-2,4-pentanediol (racemic).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.65→48.43 Å / Num. obs: 140288 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AK1

5ak1
PDB Unreleased entry


Resolution: 1.65→48.43 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.545 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19855 6940 4.9 %RANDOM
Rwork0.14637 ---
obs0.14901 133265 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.695 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å20 Å2
2--0.7 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.65→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7241 0 118 923 8282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027681
X-RAY DIFFRACTIONr_bond_other_d0.0020.026887
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.94410487
X-RAY DIFFRACTIONr_angle_other_deg0.972315821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54923.566373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.761151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0971553
X-RAY DIFFRACTIONr_chiral_restr0.0910.21112
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021887
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_it2.1781.9413742
X-RAY DIFFRACTIONr_mcbond_other2.1751.9413741
X-RAY DIFFRACTIONr_mcangle_it2.5942.9124675
X-RAY DIFFRACTIONr_mcangle_other2.5962.9124676
X-RAY DIFFRACTIONr_scbond_it2.5832.1753939
X-RAY DIFFRACTIONr_scbond_other2.5792.1753939
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.943.1785797
X-RAY DIFFRACTIONr_long_range_B_refined4.77117.949711
X-RAY DIFFRACTIONr_long_range_B_other3.89117.1239291
X-RAY DIFFRACTIONr_rigid_bond_restr2.081314568
X-RAY DIFFRACTIONr_sphericity_free34.4555315
X-RAY DIFFRACTIONr_sphericity_bonded9.352514946
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 500 -
Rwork0.267 9827 -
obs--99.28 %

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