[English] 日本語
Yorodumi
- PDB-6shd: Structure of the GH76A alpha-1,6-mannanase from Salegentibacter s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6shd
TitleStructure of the GH76A alpha-1,6-mannanase from Salegentibacter sp. HEL1_6
ComponentsAlpha-1,6-mannanase
KeywordsHYDROLASE / Mannanase / Glycoside hydrolase / GH76 / CAZyme / Mannan / Carbohydrate
Biological speciesSalegentibacter sp. Hel_I_6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHehemann, J.H. / Solanki, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Isme J / Year: 2022
Title: Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi.
Authors: Solanki, V. / Kruger, K. / Crawford, C.J. / Pardo-Vargas, A. / Danglad-Flores, J. / Hoang, K.L.M. / Klassen, L. / Abbott, D.W. / Seeberger, P.H. / Amann, R.I. / Teeling, H. / Hehemann, J.H.
History
DepositionAug 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: 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
A: Alpha-1,6-mannanase
B: Alpha-1,6-mannanase
C: Alpha-1,6-mannanase


Theoretical massNumber of molelcules
Total (without water)131,2433
Polymers131,2433
Non-polymers00
Water10,034557
1
A: Alpha-1,6-mannanase


Theoretical massNumber of molelcules
Total (without water)43,7481
Polymers43,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,6-mannanase


Theoretical massNumber of molelcules
Total (without water)43,7481
Polymers43,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-1,6-mannanase


Theoretical massNumber of molelcules
Total (without water)43,7481
Polymers43,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.261, 37.507, 187.457
Angle α, β, γ (deg.)90.000, 100.950, 90.000
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Alpha-1,6-mannanase


Mass: 43747.512 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salegentibacter sp. Hel_I_6 (bacteria) / Gene: GH76A / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M Sodium acetate pH 5.0 20 % w/v PEG 6000
PH range: 7-8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→92.02 Å / Num. obs: 87258 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Net I/σ(I): 11.3 / Num. measured all: 574248 / Scaling rejects: 49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.046.90.8453069144220.7740.3460.9152.699.8
10.77-92.025.30.05833636300.9940.0270.06424.696.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K7X

3k7x


Resolution: 2→55.091 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.34
RfactorNum. reflection% reflection
Rfree0.202 1999 2.29 %
Rwork0.1458 --
obs0.1471 87169 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.62 Å2 / Biso mean: 39.0577 Å2 / Biso min: 10.76 Å2
Refinement stepCycle: final / Resolution: 2→55.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8070 0 0 557 8627
Biso mean---41.73 -
Num. residues----1014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.27431420.17716038100
2.05-2.10550.25431430.1625602299
2.1055-2.16740.21821410.1497599899
2.1674-2.23740.19761420.1441599499
2.2374-2.31730.26061400.1641597798
2.3173-2.41010.22721420.14696047100
2.4101-2.51980.21981410.1436607499
2.5198-2.65270.20091430.1379604699
2.6527-2.81880.20251450.1483602799
2.8188-3.03650.22611410.166129100
3.0365-3.3420.20181440.1534609799
3.342-3.82550.18581460.1293616799
3.8255-4.81930.16731410.1206616499
4.8193-55.0910.19381480.1631639099

+
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