[English] 日本語
Yorodumi
- PDB-6zbw: Structure of the D125N mutant of the catalytic domain of the Baci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zbw
TitleStructure of the D125N mutant of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6-alpha-manno-cyclophellitol trisaccharide inhibitor
ComponentsAlpha-1,6-mannanase
KeywordsHYDROLASE / mannanase / cyclophellitol
Function / homology
Function and homology information


carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Six-hairpin glycosidase superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
6alpha-alpha-mannobiose / Chem-PBW / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDavies, G.J. / Offen, W.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004819/1 United Kingdom
CitationJournal: Chemistry / Year: 2021
Title: Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on alpha-1,6 Mannanases.
Authors: Schroder, S.P. / Offen, W.A. / Males, A. / Jin, Y. / de Boer, C. / Enotarpi, J. / Marino, L. / van der Marel, G.A. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Davies, G.J.
History
DepositionJun 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.3Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-1,6-mannanase
B: Alpha-1,6-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,42914
Polymers81,8602
Non-polymers1,57012
Water7,873437
1
A: Alpha-1,6-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7157
Polymers40,9301
Non-polymers7856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,6-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7157
Polymers40,9301
Non-polymers7856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.861, 66.422, 98.892
Angle α, β, γ (deg.)90.000, 100.130, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Alpha-1,6-mannanase


Mass: 40929.875 Da / Num. of mol.: 2 / Mutation: R341Q, D125N
Source method: isolated from a genetically manipulated source
Details: N-terminally His-tagged catalytic domain of BcGH76 with mutations D125N and R341Q
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: aman6 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: Q9Z4P9
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PBW / (1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol


Mass: 194.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium nitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→54.87 Å / Num. obs: 109221 / % possible obs: 99.4 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rpim(I) all: 0.029 / Net I/σ(I): 6.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5306 / CC1/2: 0.633 / Rpim(I) all: 0.629 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D4A

4d4a


Resolution: 1.4→48.72 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.286 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THERE ARE REGIONS OF UNMODELLED DENSITY NEAR THE SIDE CHAINS OF ASN277, GLU325 AND HIS308.
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 5531 5.1 %RANDOM
Rwork0.1536 ---
obs0.1564 103667 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.75 Å2 / Biso mean: 19.224 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å20.9 Å2
2---0.26 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.4→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5269 0 100 439 5808
Biso mean--20.96 30.66 -
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135603
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174705
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.6527636
X-RAY DIFFRACTIONr_angle_other_deg1.6481.59710928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6624.507304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81415810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7761513
X-RAY DIFFRACTIONr_chiral_restr0.10.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021230
X-RAY DIFFRACTIONr_rigid_bond_restr3.862310308
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 363 -
Rwork0.337 7571 -
all-7934 -
obs--98.42 %

+
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