[English] 日本語
Yorodumi
- PDB-8rg4: Crystal structure of PbFucA from Planctomycetes bacterium K23_9 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rg4
TitleCrystal structure of PbFucA from Planctomycetes bacterium K23_9 in P 21 21 21
ComponentsGlycoside-hydrolase family GH114 TIM-barrel domain-containing protein
KeywordsHYDROLASE / Fucoidan / endofucoidanase / endofuconase / GH168 / glycosyl hydrolase
Function / homologyHypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
Function and homology information
Biological speciesPlanctomycetes bacterium K23_9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.404 Å
AuthorsPerez-Cruz, C. / Moraleda-Montoya, A. / Liebana, R. / Lorizate, M. / Arrizabalaga, U. / Garcia-Alija, M. / Terrones, O. / Contreras, F.X. / Guerin, M.E. / Trastoy, B. / Alonso-Saez, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other government Spain
CitationJournal: Nat Commun / Year: 2024
Title: Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota.
Authors: Perez-Cruz, C. / Moraleda-Montoya, A. / Liebana, R. / Terrones, O. / Arrizabalaga, U. / Garcia-Alija, M. / Lorizate, M. / Martinez Gascuena, A. / Garcia-Alvarez, I. / Nieto-Garai, J.A. / ...Authors: Perez-Cruz, C. / Moraleda-Montoya, A. / Liebana, R. / Terrones, O. / Arrizabalaga, U. / Garcia-Alija, M. / Lorizate, M. / Martinez Gascuena, A. / Garcia-Alvarez, I. / Nieto-Garai, J.A. / Olazar-Intxausti, J. / Rodriguez-Colinas, B. / Mann, E. / Chiara, J.L. / Contreras, F.X. / Guerin, M.E. / Trastoy, B. / Alonso-Saez, L.
History
DepositionDec 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4783
Polymers43,3541
Non-polymers1242
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint7 kcal/mol
Surface area15450 Å2
Unit cell
Length a, b, c (Å)50.983, 84.868, 90.344
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein


Mass: 43353.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomycetes bacterium K23_9 (bacteria)
Gene: K239x_02140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A517NMB4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Microseeding of PbFucA-1 0.12 M ethylene glycols, 0.1 M buffer system 2 pH 7.5, 30% v/v precipitant mix 2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.404→9.989 Å / Num. obs: 76431 / % possible obs: 99.02 % / Redundancy: 13.2 % / Biso Wilson estimate: 14.3 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07903 / Rrim(I) all: 0.08231 / Net I/av σ(I): 19.63 / Net I/σ(I): 19.63
Reflection shellResolution: 1.404→1.454 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.07903 / Num. unique obs: 76431 / CC1/2: 0.999 / CC star: 1 / % possible all: 99.02

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.404→9.989 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1641 3837 5.02 %0.1635
Rwork0.1429 ---
obs0.144 76417 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.3 Å2
Refinement stepCycle: LAST / Resolution: 1.404→9.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 8 343 3261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008305
X-RAY DIFFRACTIONf_angle_d1.005412
X-RAY DIFFRACTIONf_dihedral_angle_d5.705403
X-RAY DIFFRACTIONf_chiral_restr0.082413
X-RAY DIFFRACTIONf_plane_restr0.009535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.404-1.420.26191090.19982257X-RAY DIFFRACTION83
1.42-1.440.20821380.15392661X-RAY DIFFRACTION100
1.44-1.460.17511230.14742696X-RAY DIFFRACTION100
1.46-1.480.18831520.14122635X-RAY DIFFRACTION100
1.48-1.50.18061300.13772722X-RAY DIFFRACTION100
1.5-1.530.19161420.12582657X-RAY DIFFRACTION100
1.53-1.550.15481490.1182652X-RAY DIFFRACTION100
1.55-1.580.1381470.11212670X-RAY DIFFRACTION100
1.58-1.610.15841380.11532662X-RAY DIFFRACTION100
1.61-1.640.16591350.11852716X-RAY DIFFRACTION100
1.64-1.670.14061600.11782656X-RAY DIFFRACTION100
1.67-1.710.14681540.11952684X-RAY DIFFRACTION100
1.71-1.750.16991310.12082689X-RAY DIFFRACTION100
1.75-1.790.16391530.12682668X-RAY DIFFRACTION100
1.79-1.840.15011350.12672714X-RAY DIFFRACTION100
1.84-1.890.161480.13232705X-RAY DIFFRACTION100
1.89-1.950.1591510.13342666X-RAY DIFFRACTION100
1.95-2.020.17541490.13532690X-RAY DIFFRACTION100
2.02-2.10.16221490.13722695X-RAY DIFFRACTION100
2.1-2.20.15371460.13532715X-RAY DIFFRACTION100
2.2-2.310.17571500.13842726X-RAY DIFFRACTION100
2.31-2.450.14631410.13472704X-RAY DIFFRACTION100
2.45-2.640.1461290.1462733X-RAY DIFFRACTION100
2.64-2.90.18371430.14812757X-RAY DIFFRACTION100
2.9-3.310.1631280.1632768X-RAY DIFFRACTION100
3.31-4.120.16731480.15122796X-RAY DIFFRACTION100
4.12-9.9890.16431590.1642886X-RAY DIFFRACTION100

+
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