[English] 日本語
Yorodumi
- PDB-8sky: Crystal structure of YisK from Bacillus subtilis in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sky
TitleCrystal structure of YisK from Bacillus subtilis in complex with oxalate
ComponentsFumarylacetoacetate hydrolase family protein
KeywordsHYDROLASE / fumarylacetoacetate hydrolase / decarboxylase / elongasome
Function / homologyFumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / isomerase activity / hydrolase activity / : / OXALATE ION / Fumarylacetoacetate hydrolase family protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKrieger, I.V. / Chemelewski, V. / Guo, T. / Sperber, A. / Herman, J. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationA-0015 United States
CitationJournal: J.Bacteriol. / Year: 2024
Title: Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization.
Authors: Guo, T. / Sperber, A.M. / Krieger, I.V. / Duan, Y. / Chemelewski, V.R. / Sacchettini, J.C. / Herman, J.K.
History
DepositionApr 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fumarylacetoacetate hydrolase family protein
B: Fumarylacetoacetate hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3876
Polymers69,1012
Non-polymers2864
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-25 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.336, 94.845, 123.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 Fumarylacetoacetate hydrolase family protein


Mass: 34550.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4122_0586 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6X359
#2: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M AmSO4, 25% (w/v) PEG-4000 and 15% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.4→48.21 Å / Num. obs: 24631 / % possible obs: 99 % / Redundancy: 11.5 % / Biso Wilson estimate: 45.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.041 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.46 / Num. unique obs: 2351 / CC1/2: 0.386 / Rpim(I) all: 0.632 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROC1.18.2_3874data processing
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.21 Å / SU ML: 0.3164 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2364 1215 4.95 %
Rwork0.1891 23355 -
obs0.1914 24570 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.91 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 0 14 117 4801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764773
X-RAY DIFFRACTIONf_angle_d1.17136440
X-RAY DIFFRACTIONf_chiral_restr0.0851731
X-RAY DIFFRACTIONf_plane_restr0.0088833
X-RAY DIFFRACTIONf_dihedral_angle_d21.16981812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.34491310.2872369X-RAY DIFFRACTION92.11
2.5-2.610.34371250.25772528X-RAY DIFFRACTION98.22
2.61-2.750.31151360.22832580X-RAY DIFFRACTION100
2.75-2.920.31421330.21522582X-RAY DIFFRACTION100
2.92-3.140.25671350.21642600X-RAY DIFFRACTION100
3.14-3.460.22841420.19322616X-RAY DIFFRACTION100
3.46-3.960.22311460.17252616X-RAY DIFFRACTION100
3.96-4.990.19781230.15352676X-RAY DIFFRACTION100
4.99-48.210.2041440.1782788X-RAY DIFFRACTION99.69

+
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