[English] 日本語
Yorodumi
- PDB-6tn6: X-ray structure of the endo-beta-1,4-mannanase from Thermotoga pe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tn6
TitleX-ray structure of the endo-beta-1,4-mannanase from Thermotoga petrophila
ComponentsMannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
KeywordsHYDROLASE / Mannanase / hyperthermophile
Function / homology
Function and homology information


mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / metabolic process
Similarity search - Function
Carbohydrate binding module 27 / Carbohydrate binding module 27 / Mannan endo-1,4-beta-mannosidase-like / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / CARBONATE ION / DI(HYDROXYETHYL)ETHER / Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
Similarity search - Component
Biological speciesThermotoga petrophila RKU-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
Authorsda Silva, V.M. / Squina, F.M. / Sperenca, M. / Martin, L. / Muniz, J.R.C. / Garcia, W. / Nicolet, Y.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2020
Title: High-resolution structure of a modular hyperthermostable endo-beta-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain.
Authors: da Silva, V.M. / Cabral, A.D. / Speranca, M.A. / Squina, F.M. / Muniz, J.R.C. / Martin, L. / Nicolet, Y. / Garcia, W.
History
DepositionDec 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,30221
Polymers73,8311
Non-polymers1,47120
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-10 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.710, 174.710, 174.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-1475-

HOH

21A-1498-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5


Mass: 73830.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga petrophila RKU-1 (bacteria) / Gene: Tpet_1542 / Production host: Escherichia coli (E. coli)
References: UniProt: A5IMX7, mannan endo-1,4-beta-mannosidase

-
Non-polymers , 10 types, 522 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen D12 condition

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→46.693 Å / Num. obs: 303865 / % possible obs: 99.9 % / Redundancy: 6.67 % / CC1/2: 1 / Rrim(I) all: 0.043 / Rsym value: 0.042 / Net I/σ(I): 23.26
Reflection shellResolution: 1.45→1.49 Å / Num. unique obs: 11434 / CC1/2: 0.52

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXv1.15.2-3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZ9

3pz9


Resolution: 1.45→46.693 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 17.81
RfactorNum. reflection% reflection
Rfree0.1506 15209 5.01 %
Rwork0.1374 --
obs0.1381 155320 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.37 Å2 / Biso mean: 33.456 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 1.45→46.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 208 504 4485
Biso mean--71.31 45.32 -
Num. residues----465
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4501-1.46660.31925020.3486940897
1.4666-1.48380.33975030.3268968199
1.4838-1.50190.31995070.3119957699
1.5019-1.52090.30545000.306952899
1.5209-1.54090.32665070.31389678100
1.5409-1.56210.29235140.2869734100
1.5621-1.58440.27325070.27659604100
1.5844-1.6080.29155120.25549709100
1.608-1.63320.25415070.2429629100
1.6332-1.65990.21785130.22649628100
1.6599-1.68860.24255060.212963399
1.6886-1.71930.22145060.20469592100
1.7193-1.75230.20475120.1891966899
1.7523-1.78810.19374970.1774956399
1.7881-1.8270.18315040.17329611100
1.827-1.86950.18875180.16549756100
1.8695-1.91620.17015020.15689624100
1.9162-1.9680.16255090.14619603100
1.968-2.0260.16475060.14019694100
2.026-2.09130.1585150.12719611100
2.0913-2.16610.15195110.1244962099
2.1661-2.25280.12295020.11499564100
2.2528-2.35530.12965030.11619696100
2.3553-2.47950.12845120.11019666100
2.4795-2.63490.11695050.10439635100
2.6349-2.83830.12425100.11269691100
2.8383-3.12380.13395040.1173957699
3.1238-3.57570.12135040.1129951098
3.5757-4.50450.10825050.10079640100
4.5045-46.6930.15575060.1407952898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7109-0.5587-0.89312.1167-0.13793.06420.07420.12060.0841-0.0383-0.05370.0379-0.0311-0.1194-0.03860.13830.00070.01950.1638-0.01220.185547.363585.8096105.2065
20.6585-0.2739-0.22260.67780.16680.3369-0.01340.00340.00050.0537-0.02020.00370.019-0.00160.03410.2077-0.00060.02260.198-0.02170.190150.6874.9822108.1497
34.14590.76970.79282.73660.51872.9019-0.0319-0.16260.20960.0796-0.0106-0.382-0.11090.34050.02820.23230.02760.05020.2325-0.02110.3382.733471.430993.3678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 84 )A30 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 408 )A85 - 408
3X-RAY DIFFRACTION3chain 'A' and (resid 409 through 494 )A409 - 494

+
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