[English] 日本語
Yorodumi
- PDB-8q29: TtX122A - A domain of unknown function from the Teredinibacter tu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q29
TitleTtX122A - A domain of unknown function from the Teredinibacter turnerae protein TERTU_3803
ComponentsGluconolactonase domain protein
KeywordsUNKNOWN FUNCTION / beta-jelly roll fold / X122 / CAZy / Teredinibacter turnerae
Function / homology
Function and homology information


cellulose binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
: / Cip1-like, core domain / Domain of unknown function DUF1587 / Domain of unknown function DUF1588 / Domain of unknown function DUF1592 / Domain of unknown function DUF1595 / Protein of unknown function (DUF1587) / Protein of unknown function (DUF1588) / Protein of unknown function (DUF1592) / Protein of unknown function (DUF1595) ...: / Cip1-like, core domain / Domain of unknown function DUF1587 / Domain of unknown function DUF1588 / Domain of unknown function DUF1592 / Domain of unknown function DUF1595 / Protein of unknown function (DUF1587) / Protein of unknown function (DUF1588) / Protein of unknown function (DUF1592) / Protein of unknown function (DUF1595) / Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Senescence marker protein-30 (SMP-30) / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Soluble quinoprotein glucose/sorbosone dehydrogenase / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / NHL repeat profile. / NHL repeat / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Cytochrome C oxidase, cbb3-type, subunit III / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-bladed beta-propeller, TolB-like / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Gluconolactonase domain protein
Similarity search - Component
Biological speciesTeredinibacter turnerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsRajagopal, B.S. / Hemsworth, G.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N019970/1 United Kingdom
CitationJournal: Iucrj / Year: 2024
Title: Structural dissection of two redox proteins from the shipworm symbiont Teredinibacter turnerae.
Authors: Rajagopal, B.S. / Yates, N. / Smith, J. / Paradisi, A. / Tetard-Jones, C. / Willats, W.G.T. / Marcus, S. / Knox, J.P. / Firdaus-Raih, M. / Henrissat, B. / Davies, G.J. / Walton, P.H. / ...Authors: Rajagopal, B.S. / Yates, N. / Smith, J. / Paradisi, A. / Tetard-Jones, C. / Willats, W.G.T. / Marcus, S. / Knox, J.P. / Firdaus-Raih, M. / Henrissat, B. / Davies, G.J. / Walton, P.H. / Parkin, A. / Hemsworth, G.R.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gluconolactonase domain protein
B: Gluconolactonase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,45414
Polymers54,9042
Non-polymers55012
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-37 kcal/mol
Surface area17920 Å2
Unit cell
Length a, b, c (Å)48.081, 75.167, 69.074
Angle α, β, γ (deg.)90.000, 107.423, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Gluconolactonase domain protein


Mass: 27451.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Teredinibacter turnerae (bacteria) / Gene: TERTU_3803 / Production host: Escherichia coli (E. coli) / References: UniProt: C5BSV8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.1 M magnesium acetate, 15-25% PEG-3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97952 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.5→49.55 Å / Num. obs: 73564 / % possible obs: 98.2 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.037 / Rrim(I) all: 0.06 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.22-49.554.10.0254600.9990.0190.032
1.5-1.534.60.40935530.8810.3220.523

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
SHELXphasing
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.5→49.55 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.399 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1563 3529 4.799 %
Rwork0.1122 70010 -
all0.114 --
obs-73539 98.019 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.013 Å2
Baniso -1Baniso -2Baniso -3
1--0.381 Å20 Å20.326 Å2
2--0.727 Å2-0 Å2
3----0.461 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 30 390 4176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123959
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163450
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.6475407
X-RAY DIFFRACTIONr_angle_other_deg0.6641.5937934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9525509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.84512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89410578
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.37110220
X-RAY DIFFRACTIONr_chiral_restr0.1050.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02989
X-RAY DIFFRACTIONr_nbd_refined0.1950.2699
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.23368
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21920
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2293
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.210
X-RAY DIFFRACTIONr_nbd_other0.1870.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_mcbond_it7.0571.9221958
X-RAY DIFFRACTIONr_mcbond_other7.0291.9221958
X-RAY DIFFRACTIONr_mcangle_it9.2253.4652451
X-RAY DIFFRACTIONr_mcangle_other9.2283.4662452
X-RAY DIFFRACTIONr_scbond_it8.5822.12001
X-RAY DIFFRACTIONr_scbond_other8.582.1012002
X-RAY DIFFRACTIONr_scangle_it11.2963.7582942
X-RAY DIFFRACTIONr_scangle_other11.2943.7582943
X-RAY DIFFRACTIONr_lrange_it14.52521.8894443
X-RAY DIFFRACTIONr_lrange_other14.52421.8884443
X-RAY DIFFRACTIONr_rigid_bond_restr4.77737409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2112730.1595058X-RAY DIFFRACTION96.8216
1.539-1.5810.1812350.144984X-RAY DIFFRACTION97.5879
1.581-1.6270.1892220.1324905X-RAY DIFFRACTION97.3419
1.627-1.6770.1752080.114771X-RAY DIFFRACTION97.8385
1.677-1.7320.1642390.1034584X-RAY DIFFRACTION97.9488
1.732-1.7920.1782190.0974476X-RAY DIFFRACTION98.1191
1.792-1.860.1562310.0924289X-RAY DIFFRACTION98.4964
1.86-1.9360.1512280.0844147X-RAY DIFFRACTION98.3809
1.936-2.0220.1322080.0883996X-RAY DIFFRACTION98.5929
2.022-2.120.1492220.0953780X-RAY DIFFRACTION98.62
2.12-2.2350.1381870.0923641X-RAY DIFFRACTION98.8381
2.235-2.370.1471630.0923461X-RAY DIFFRACTION98.7197
2.37-2.5330.1491800.0913236X-RAY DIFFRACTION99.0719
2.533-2.7360.1531360.1033036X-RAY DIFFRACTION99.0012
2.736-2.9960.1581450.1042796X-RAY DIFFRACTION98.9236
2.996-3.3480.1541470.122481X-RAY DIFFRACTION98.4638
3.348-3.8630.151080.1212214X-RAY DIFFRACTION97.3993
3.863-4.7240.13790.1171856X-RAY DIFFRACTION95.8395
4.724-6.650.18550.1611473X-RAY DIFFRACTION97.201
6.65-49.550.212440.212826X-RAY DIFFRACTION95.9206

+
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