[English] 日本語
Yorodumi
- PDB-8bqa: CjCel5B endo-glucanase bound to CB665 covalent inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bqa
TitleCjCel5B endo-glucanase bound to CB665 covalent inhibitor
ComponentsEndoglucanase
KeywordsHYDROLASE / Carbohydrate / inhibitor / covalent / cellulase
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II ...Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-RBH / alpha-D-xylopyranose / Chem-YLL / Endoglucanase
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMcGregor, N.G.S. / de Boer, C. / Overkleeft, H.S. / Davies, G.J.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
European Research Council (ERC)2020-SyG-951231European Union
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: A Multiplexing Activity-Based Protein-Profiling Platform for Dissection of a Native Bacterial Xyloglucan-Degrading System.
Authors: McGregor, N.G.S. / de Boer, C. / Foucart, Q.P.O. / Beenakker, T. / Offen, W.A. / Codee, J.D.C. / Willems, L.I. / Overkleeft, H.S. / Davies, G.J.
History
DepositionNov 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 2.0Jan 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
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_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2594
Polymers33,5191
Non-polymers7403
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.490, 51.830, 64.560
Angle α, β, γ (deg.)90.000, 110.427, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Endoglucanase


Mass: 33519.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Gene: cel5B, CJA_2983 / Production host: Escherichia coli B (bacteria) / References: UniProt: B3PCS3, cellulase
#2: Chemical ChemComp-RBH / ~{N}-[(2~{S},3~{S},4~{S},5~{R})-2-(hydroxymethyl)-4,5,6-tris(oxidanyl)oxan-3-yl]-2-oxidanyl-ethanamide


Mass: 395.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H27N4O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-YLL / (1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL


Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.19 % / Description: Plate clusters
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PS: 10 mg/mL in 5 mM Na-MOPS pH 7.5, 25 mM NaCl 1:1 with WS containing 0.2 M LiCl, 20% PEG3350
PH range: 5.5-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.67→32.92 Å / Num. obs: 32027 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.08 / Rrim(I) all: 0.198 / Net I/σ(I): 6.6
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.556 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1580 / CC1/2: 0.341 / Rpim(I) all: 1.095 / Rrim(I) all: 2.784 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tvn

1tvn


Resolution: 1.67→32.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.219 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1561 4.876 %0.05
Rwork0.1857 30450 --
all0.188 ---
obs-32011 97.467 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.653 Å2
Baniso -1Baniso -2Baniso -3
1-0.774 Å20 Å21.597 Å2
2---1.93 Å20 Å2
3----0.027 Å2
Refinement stepCycle: LAST / Resolution: 1.67→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 36 197 2526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182147
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.6273268
X-RAY DIFFRACTIONr_angle_other_deg1.4351.5814918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09824.454119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33115341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.526156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
X-RAY DIFFRACTIONr_nbd_refined0.2070.2527
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22086
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21195
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2187
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.28
X-RAY DIFFRACTIONr_nbd_other0.1430.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.216
X-RAY DIFFRACTIONr_mcbond_it1.5942.4161191
X-RAY DIFFRACTIONr_mcbond_other1.5932.4131190
X-RAY DIFFRACTIONr_mcangle_it2.0883.6181487
X-RAY DIFFRACTIONr_mcangle_other2.0873.6211488
X-RAY DIFFRACTIONr_scbond_it2.1382.5751202
X-RAY DIFFRACTIONr_scbond_other2.1372.5751203
X-RAY DIFFRACTIONr_scangle_it3.0353.81781
X-RAY DIFFRACTIONr_scangle_other3.0343.81782
X-RAY DIFFRACTIONr_lrange_it3.8329.2422883
X-RAY DIFFRACTIONr_lrange_other3.77228.9852845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7130.361940.3422216X-RAY DIFFRACTION96.4107
1.713-1.760.3221160.3072175X-RAY DIFFRACTION96.3415
1.76-1.8110.3311290.3022059X-RAY DIFFRACTION96.3877
1.811-1.8670.338950.2742047X-RAY DIFFRACTION96.9231
1.867-1.9280.2981280.2771968X-RAY DIFFRACTION96.8577
1.928-1.9960.255760.2241941X-RAY DIFFRACTION97.0645
1.996-2.0710.2441120.2011872X-RAY DIFFRACTION96.875
2.071-2.1550.216900.1871793X-RAY DIFFRACTION97.5142
2.155-2.2510.226970.1861691X-RAY DIFFRACTION97.0684
2.251-2.3610.23870.1721659X-RAY DIFFRACTION97.5964
2.361-2.4880.226790.1641570X-RAY DIFFRACTION97.574
2.488-2.6390.24640.1631499X-RAY DIFFRACTION98.2401
2.639-2.8210.204690.1661435X-RAY DIFFRACTION98.3649
2.821-3.0460.241800.1651319X-RAY DIFFRACTION98.6601
3.046-3.3360.239420.1871231X-RAY DIFFRACTION98.8354
3.336-3.7290.23610.1681118X-RAY DIFFRACTION99.0756
3.729-4.3030.155370.1461002X-RAY DIFFRACTION99.2359
4.303-5.2630.151540.143818X-RAY DIFFRACTION98.8662
5.263-7.4150.139260.145660X-RAY DIFFRACTION99.2764
7.415-32.920.199250.148377X-RAY DIFFRACTION97.8102

+
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