[English] 日本語
Yorodumi
- PDB-5afe: Medium Resolution structure of the C-terminal family 65 Carbohydr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5afe
TitleMedium Resolution structure of the C-terminal family 65 Carbohydrate Binding Module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens with a bound xyloglucan heptasaccharide (XXXG)
ComponentsENDOGLUCANASE CEL5A
KeywordsHYDROLASE / CBM65B / CARBOHYDRATE BINDING MODULE / ENDOGLUCANASE CEL5A / EUBACTERIUM CELLULOSOLVENS / PLANT CELL WALL DEGRADATION / XYLOGUCAN HEPTASACCHARIDE
Function / homology
Function and homology information


beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Jelly Rolls - #1070 / Carbohydrate binding module 65 domain 1 / Carbohydrate binding module 65 domain 1 / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Endoglucanase cel5A
Similarity search - Component
Biological speciesEUBACTERIUM CELLULOSOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVenditto, I. / Fontes, C.M.G.A. / Gilbert, H.J. / Najmudin, S.
Citation
Journal: To be Published
Title: Understanding How Noncatalytic Carbohydrate Binding Modules Can Display Specificity for Xyloglucan
Authors: Luis, A.S. / Venditto, I. / Basle, A. / Prates, J.A.M. / Ferreira, L.M.A. / Temple, M. / Rogowski, A. / Xue, J. / Knox, J.P. / Fontes, C.M.G.A. / Gilbert, H.J. / Najmudin, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of the C-Terminal Family 65 Carbohydrate-Binding Module (Cbm65B) of Endoglucanase Cel5A from Eubacterium Cellulosolvens.
Authors: Venditto, I. / Basle, A. / Luis, A.S. / Temple, M.J. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Gilbert, H.J. / Najmudin, S.
History
DepositionJan 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_special_symmetry / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOGLUCANASE CEL5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2133
Polymers15,9581
Non-polymers1,2552
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.960, 58.960, 117.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

-
Components

#1: Protein ENDOGLUCANASE CEL5A


Mass: 15957.568 Da / Num. of mol.: 1
Fragment: C-TERMINAL FAMILY 65 CARBOHYDRATE BINDING MODULE (CBM65B), UNP RESIDUES 578-721
Source method: obtained synthetically / Source: (synth.) EUBACTERIUM CELLULOSOLVENS (bacteria) / References: UniProt: Q3LHN3, cellulase
#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2-2/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCITRIC ACID (CIT): FROM THE CRYSTALLISATION BUFFER XYLOPYRANOSE (XYS): PART OF THE XYLOGLUCAN ...CITRIC ACID (CIT): FROM THE CRYSTALLISATION BUFFER XYLOPYRANOSE (XYS): PART OF THE XYLOGLUCAN HEPTASACCHARIDE XXXG BETA-D-GLUCOSE (BGC): PART OF THE XYLOGLUCAN HEPTASACCHARIDE XXXG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30%(W/V) PEG 4000 CO-CRYSTALLISED WITH 10 MM OF HEPTASACCHARIDE XXXG CRYOPROTECTAN WAS 30% GLYCEROL ADDED TO ABOVE CRYSTALLISATION BUFFER

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→58.96 Å / Num. obs: 6535 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 2.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BA6

4ba6


Resolution: 2.6→52.66 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 41.99 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED PDB_REDO WAS USED IN THE PENULTIMATE ROUND OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.30613 303 4.7 %RANDOM
Rwork0.24861 ---
obs0.25122 6206 95.3 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→52.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 85 28 1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021095
X-RAY DIFFRACTIONr_bond_other_d0.0010.02979
X-RAY DIFFRACTIONr_angle_refined_deg1.1122.0341500
X-RAY DIFFRACTIONr_angle_other_deg0.64532275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1785123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55625.43546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15515157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.238151
X-RAY DIFFRACTIONr_chiral_restr0.0680.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02226
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_it0.963.061495
X-RAY DIFFRACTIONr_mcbond_other0.9623.055494
X-RAY DIFFRACTIONr_mcangle_it1.7684.581617
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.323.659600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 19 -
Rwork0.453 448 -
obs--96.09 %
Refinement TLS params.Method: refined / Origin x: 19.54 Å / Origin y: -0.918 Å / Origin z: 4.981 Å
111213212223313233
T0.5555 Å2-0.0672 Å2-0.066 Å2-0.5138 Å20.0109 Å2--0.029 Å2
L3.947 °2-1.4483 °2-0.7012 °2-4.0016 °2-0.0989 °2--5.0989 °2
S0.1421 Å °-0.0192 Å °-0.1411 Å °0.0073 Å °0.0659 Å °0.2304 Å °0.2109 Å °-0.2348 Å °-0.2081 Å °

+
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