[English] 日本語
Yorodumi
- PDB-5nok: Polysaccharide Lyase BACCELL_00875 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nok
TitlePolysaccharide Lyase BACCELL_00875
ComponentsBACCELL_00875
KeywordsLYASE / Polysaccharide Lyase / Arabinogalactan / L-Rhamnose / Glucuronic Acid
Function / homologySix-hairpin glycosidase superfamily / carbohydrate metabolic process / Six-hairpin glycosidase
Function and homology information
Biological speciesBacteroides cellulosilyticus DSM 14838 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsCartmell, A. / Munoz-Munoz, J. / Terrapon, N. / Basle, A. / Henrissat, B. / Gilbert, H.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council322820 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2017
Title: An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins.
Authors: Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Basle, A. / Henrissat, B. / Gilbert, H.J.
History
DepositionApr 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BACCELL_00875
B: BACCELL_00875
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6093
Polymers161,4142
Non-polymers1951
Water4,396244
1
A: BACCELL_00875


Theoretical massNumber of molelcules
Total (without water)80,7071
Polymers80,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BACCELL_00875
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9022
Polymers80,7071
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.730, 116.730, 228.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein BACCELL_00875


Mass: 80706.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides cellulosilyticus DSM 14838 (bacteria)
Gene: BACCELL_00875 / Production host: Escherichia coli (E. coli) / References: UniProt: E2N9D0
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG1500, 0.1 M MMT buffer, pH 4.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.24→47.48 Å / Num. obs: 76640 / % possible obs: 100 % / Redundancy: 43.2 % / Rmerge(I) obs: 0.0131 / Net I/σ(I): 10.6
Reflection shellResolution: 2.24→2.29 Å / Rmerge(I) obs: 0.3201

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→47.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.078 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24925 3842 5 %RANDOM
Rwork0.19499 ---
obs0.19768 72698 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.015 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å2-0 Å2
2--1.09 Å2-0 Å2
3----2.18 Å2
Refinement stepCycle: 1 / Resolution: 2.24→103.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10688 0 12 244 10944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910971
X-RAY DIFFRACTIONr_bond_other_d0.0020.029700
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.95114892
X-RAY DIFFRACTIONr_angle_other_deg0.978322418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77151334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57423.872563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.217151652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2511574
X-RAY DIFFRACTIONr_chiral_restr0.0870.21562
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212433
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022425
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_it2.2853.9775345
X-RAY DIFFRACTIONr_mcbond_other2.2843.9775344
X-RAY DIFFRACTIONr_mcangle_it3.475.9596676
X-RAY DIFFRACTIONr_mcangle_other3.475.9596677
X-RAY DIFFRACTIONr_scbond_it2.8514.2445626
X-RAY DIFFRACTIONr_scbond_other2.8514.2445626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5676.2448217
X-RAY DIFFRACTIONr_long_range_B_refined6.02146.10512158
X-RAY DIFFRACTIONr_long_range_B_other6.02146.09812157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 295 -
Rwork0.289 5268 -
obs--99.98 %

+
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