[English] 日本語
Yorodumi
- PDB-7nl5: Structure of the catalytic domain of the Bacillus circulans alpha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nl5
TitleStructure 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 / epoxide
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
Chem-UKQ / Chem-UKT / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchroeder, S. / 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. ...Schroeder, S. / 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.
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
DepositionFeb 22, 2021Deposition 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 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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)41,6284
Polymers40,9311
Non-polymers6973
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint9 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.521, 65.415, 49.442
Angle α, β, γ (deg.)90.000, 101.900, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Alpha-1,6-mannanase


Mass: 40930.859 Da / Num. of mol.: 1 / Mutation: R341Q
Source method: isolated from a genetically manipulated source
Details: N-terminal his-tagged catalytic domain of alpha-1,6-mannanase Aman6
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


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-UKQ / (1R,6S)-5beta-(Hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2beta,3beta,4alpha-triol / (1~{R},2~{S},3~{S},4~{R},5~{R},6~{S})-5-(hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2,3,4-triol / epi-manno-cyclophellitol


Mass: 176.167 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H12O5
#4: Chemical ChemComp-UKT / (1R,2R,3R,4S,5R)-4-(hydroxymethyl)cyclohexane-1,2,3,5-tetrol / (1~{R},2~{R},3~{R},4~{S},5~{R})-4-(hydroxymethyl)cyclohexane-1,2,3,5-tetrol


Mass: 178.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium nitrate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→65.41 Å / Num. obs: 53069 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.993 / Net I/σ(I): 6.4
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 2353 / CC1/2: 0.742

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D4A

4d4a


Resolution: 1.4→48.43 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.129 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THERE IS UNMODELLED DENSITY AT THE N-TERMINAL AND C-TERMINAL RESIDUES SER39 AND ILE375, AND BETWEEN RESIDUES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THERE IS UNMODELLED DENSITY AT THE N-TERMINAL AND C-TERMINAL RESIDUES SER39 AND ILE375, AND BETWEEN RESIDUES 355 AND 358. THERE IS A REGION OF UNMODELLED DENSITY BETWEEN THE SIDE CHAINS OF LYS273 AND ASN206 OF A SYMMETRY RELATED MOLECULE. THE -1 SUBSITE IS MODELLED WITH 2 PART-OCCUPANCY MANNO-EPOXIDES (EACH AT 0.4), ONE COVALENTLY REACTED AND ONE UNREACTED, WHICH ARE BOTH BOUND TO MANNOBIOSE IN THE -2 AND -3 SUBSITES. THERE IS ALSO A MANNOBIOSE MODELLED AT AN OCCUPANCY OF 0.2 IN THE -2 AND -3 SUBSITES.
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 2576 4.9 %RANDOM
Rwork0.1471 ---
obs0.1483 50450 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.07 Å2 / Biso mean: 16.589 Å2 / Biso min: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20.88 Å2
2--0.1 Å20 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.4→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 46 295 2999
Biso mean--17.84 29.04 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132837
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182434
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.6583883
X-RAY DIFFRACTIONr_angle_other_deg1.6911.6115599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52524.423156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04315407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.427157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02698
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 179 -
Rwork0.238 3415 -
all-3594 -
obs--91.68 %

+
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