[English] 日本語
Yorodumi
- PDB-2bvd: HOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bvd
TitleHOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE AND ACTIVITY OF A CLOSTRIDIUM THERMOCELLUM LICHENASE, CtLIC26A
ComponentsENDOGLUCANASE H
KeywordsHYDROLASE / LICHENASE / BETA-1 4 BETA-1 3 GLUCANASE / GLYCOSIDE HYDROLASE FAMILY 26
Function / homology
Function and homology information


cellulase / beta-glucosidase activity / cellulase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain ...Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / 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) / Galactose-binding-like domain superfamily / EF-hand calcium-binding domain. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-ISX / Endoglucanase H
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTaylor, E.J. / Goyal, A. / Guerreiro, C.I.P.D. / Prates, J.A.M. / Money, V.A. / Ferry, N. / Morland, C. / Planas, A. / Macdonald, J.A. / Stick, R.V. ...Taylor, E.J. / Goyal, A. / Guerreiro, C.I.P.D. / Prates, J.A.M. / Money, V.A. / Ferry, N. / Morland, C. / Planas, A. / Macdonald, J.A. / Stick, R.V. / Gilbert, H.J. / Fontes, C.M.G.A. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: How Family 26 Glycoside Hydrolases Orchestrate Catalysis on Different Polysaccharides: Structure and Activity of a Clostridium Thermocellum Lichenase, Ctlic26A.
Authors: Taylor, E.J. / Goyal, A. / Guerreiro, C.I.P.D. / Prates, J.A.M. / Money, V.A. / Ferry, N. / Morland, C. / Planas, A. / Macdonald, J.A. / Stick, R.V. / Gilbert, H.J. / Fontes, C.M.G.A. / Davies, G.J.
History
DepositionJun 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOGLUCANASE H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5402
Polymers32,2311
Non-polymers3091
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.272, 63.012, 78.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ENDOGLUCANASE H / EGH / ENDO-1 / 4-BETA-GLUCANASE / CELLULASE H / LICH26A


Mass: 32230.650 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: F1/YS / Plasmid: PCF1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16218, cellulase
#2: Sugar ChemComp-ISX / (3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)piperidin-3-yl beta-D-glucopyranoside / GLUCOSE BETA-1,3-ISOFAGAMINE / (3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)piperidin-3-yl beta-D-glucoside / (3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)piperidin-3-yl D-glucoside / (3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)piperidin-3-yl glucoside


Type: D-saccharide / Mass: 309.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H23NO8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE ...HOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE AND ACTIVITY OF A CLOSTRIDIUM THERMOCELLUM LICHENASE, CTLIC26A FIRST THREE N TERMINAL RESIDUES (MAS) ARE DERIVED FROM THE CLONING VECTOR PET21A.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 34 %
Crystal growpH: 6.5
Details: PROTEIN WAS CO-CRYSTALLIZED WITH THE LIGAND FROM 0.15 M AMMONIUM SULPHATE, 30% PEG 5K MME BUFFERED TO PH 6.5 WITH MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 5, 2005
RadiationMonochromator: SI 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 32817 / % possible obs: 99 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 17 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BV9

2bv9


Resolution: 1.6→49.09 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.357 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1633 5 %RANDOM
Rwork0.154 ---
obs0.156 30951 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 21 374 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9053348
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7855307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50923.937127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34715379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0561515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021925
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21246
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21686
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8361.51452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2522305
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66431170
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4784.51025
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.161 123
Rwork0.153 2237

+
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