[English] 日本語
Yorodumi
- PDB-5la2: The mechanism by which arabinoxylanases can recognise highly deco... -

+
Open data


ID or keywords:

Loading...

-
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
Cellulose binding, type IV / Cellulose Binding Domain Type IV / Ricin-type beta-trefoil lectin domain-like / 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. ...Cellulose binding, type IV / Cellulose Binding Domain Type IV / Ricin-type beta-trefoil lectin domain-like / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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).

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more