[English] 日本語
Yorodumi
- PDB-7kr6: Glycoside hydrolase family 16 endo-glucanase from Bacteroides ova... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kr6
TitleGlycoside hydrolase family 16 endo-glucanase from Bacteroides ovatus in complex with G4G3G-2F-DNP
ComponentsGlycoside hydrolase family 16 protein
KeywordsHYDROLASE / Inhibitor / glucanase
Function / homologyGlycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-2-deoxy-2-fluoro-alpha-D-glucopyranose / Glycoside hydrolase family 16 protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsTamura, K. / Brumer, H. / van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Orthogonal Active-Site Labels for Mixed-Linkage endo-beta-Glucanases.
Authors: Jain, N. / Tamura, K. / Dejean, G. / Van Petegem, F. / Brumer, H.
History
DepositionNov 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 27, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Glycoside hydrolase family 16 protein
BBB: Glycoside hydrolase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2014
Polymers61,1882
Non-polymers1,0132
Water6,738374
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)46.447, 84.576, 67.105
Angle α, β, γ (deg.)90.000, 93.983, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glycoside hydrolase family 16 protein


Mass: 30593.943 Da / Num. of mol.: 2 / Mutation: E148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria)
Gene: DW206_07605, DW890_00285, F3D51_00680, F3D58_00285, F3F38_18210
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y4PXW9
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-2-deoxy-2-fluoro-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 506.429 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-2-deoxy-2-fluoro-alpha-D-glucopyranose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5_2*F][a2122h-1b_1-5]/1-2-2/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp2fluoro]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M Tris pH 8.5, 25% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.56→39.4 Å / Num. obs: 143215 / % possible obs: 98.7 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 14.2
Reflection shellResolution: 1.56→1.59 Å / Num. unique obs: 6822 / CC1/2: 0.935

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NBO

5nbo


Resolution: 1.56→39.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1985 3598 4.961 %
Rwork0.1722 68931 -
all0.173 --
obs-72529 98.568 %
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: 24.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.829 Å20 Å2-2.23 Å2
2--0.966 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.56→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3737 0 66 374 4177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133931
X-RAY DIFFRACTIONr_bond_other_d0.0360.0183396
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.6565317
X-RAY DIFFRACTIONr_angle_other_deg2.7041.6067921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2355472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11625200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46515629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.786156
X-RAY DIFFRACTIONr_chiral_restr0.0820.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024398
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02820
X-RAY DIFFRACTIONr_nbd_refined0.1830.2625
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.23122
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21820
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2266
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.21
X-RAY DIFFRACTIONr_nbd_other0.1160.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.210
X-RAY DIFFRACTIONr_mcbond_it2.1772.4951894
X-RAY DIFFRACTIONr_mcbond_other2.1612.4931893
X-RAY DIFFRACTIONr_mcangle_it2.9193.7312364
X-RAY DIFFRACTIONr_mcangle_other2.9263.7322365
X-RAY DIFFRACTIONr_scbond_it2.9912.7112037
X-RAY DIFFRACTIONr_scbond_other2.9912.7112037
X-RAY DIFFRACTIONr_scangle_it4.463.9632953
X-RAY DIFFRACTIONr_scangle_other4.463.9642954
X-RAY DIFFRACTIONr_lrange_it5.33228.9964339
X-RAY DIFFRACTIONr_lrange_other5.26528.6114270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.2953010.2754927X-RAY DIFFRACTION95.8211
1.6-1.6440.2592670.2424933X-RAY DIFFRACTION98.9911
1.644-1.6920.2372500.2254820X-RAY DIFFRACTION99.0428
1.692-1.7440.2412110.2124727X-RAY DIFFRACTION98.9579
1.744-1.8010.2422470.194506X-RAY DIFFRACTION98.2634
1.801-1.8640.2192510.1894385X-RAY DIFFRACTION98.3036
1.864-1.9350.2442130.1874265X-RAY DIFFRACTION99.0927
1.935-2.0140.2182100.194107X-RAY DIFFRACTION99.2642
2.014-2.1030.232110.1913912X-RAY DIFFRACTION98.8018
2.103-2.2060.2051640.1763738X-RAY DIFFRACTION97.6721
2.206-2.3250.2042010.1643575X-RAY DIFFRACTION99.29
2.325-2.4660.2011750.1613390X-RAY DIFFRACTION99.359
2.466-2.6360.2051570.1723188X-RAY DIFFRACTION99.2582
2.636-2.8470.1911610.1722935X-RAY DIFFRACTION98.0989
2.847-3.1180.1891410.1712730X-RAY DIFFRACTION99.4114
3.118-3.4860.1911290.1712483X-RAY DIFFRACTION99.2401
3.486-4.0240.181040.1572193X-RAY DIFFRACTION98.8382
4.024-4.9250.154940.1321856X-RAY DIFFRACTION98.7342
4.925-6.9540.172820.161443X-RAY DIFFRACTION99.026
6.954-39.40.16129818X-RAY DIFFRACTION97.5807

+
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://pdbjlvh1.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