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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zbm
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 carbasugar-stabilised trisaccharide inhibitor
ComponentsAlpha-1,6-mannanase
KeywordsHYDROLASE / ENDO-ALPHA-1 / 6-MANNANASE / EPOXIDE / INHIBITOR
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
alpha-D-mannopyranose / Chem-QE8 / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 8, 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 1.5Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5735
Polymers40,9301
Non-polymers6434
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint5 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.768, 66.121, 49.397
Angle α, β, γ (deg.)90.000, 100.230, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Alpha-1,6-mannanase


Mass: 40929.875 Da / Num. of mol.: 1 / Mutation: D125N, R341Q
Source method: isolated from a genetically manipulated source
Details: Catalytic domain of BcGH76 without signal peptide and with N-terminal His tag, and with mutations D125N and R341Q
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: aman6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z4P9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-QE8 / (1~{R},2~{R},3~{R},4~{S},5~{R})-4-[[(1~{S},2~{S},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-2,3,4-tris(oxidanyl)cyclohexyl]oxymethyl]cyclohexane-1,2,3,5-tetrol


Mass: 338.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H26O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 28.43 %
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 EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.47→66.12 Å / Num. obs: 47092 / % possible obs: 99.8 % / Redundancy: 4 % / CC1/2: 0.95 / Rpim(I) all: 0.13 / Net I/σ(I): 3.1
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2333 / CC1/2: 0.676 / Rpim(I) all: 0.631 / % possible all: 99.7

-
Processing

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

4d4a


Resolution: 1.47→48.66 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.101 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.083 / 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 ASN206, HIS340 AND TYR360.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2304 4.9 %RANDOM
Rwork0.1586 ---
obs0.1616 44764 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.29 Å2 / Biso mean: 13.884 Å2 / Biso min: 6.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å21.3 Å2
2--0.31 Å20 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.47→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 42 178 2845
Biso mean--13.69 23.68 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132815
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172374
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.6513838
X-RAY DIFFRACTIONr_angle_other_deg1.6321.5995527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1565344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85824.481154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35915421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.188157
X-RAY DIFFRACTIONr_chiral_restr0.0930.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023211
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02618
X-RAY DIFFRACTIONr_rigid_bond_restr4.6235188
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 162 -
Rwork0.326 3284 -
all-3446 -
obs--99.45 %

+
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