[English] 日本語
Yorodumi
- PDB-6c32: Mycobacterium smegmatis RimJ with AcCoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c32
TitleMycobacterium smegmatis RimJ with AcCoA
ComponentsAcetyltransferase, GNAT family protein
KeywordsTRANSFERASE / GNAT / N-acetyltransferase
Function / homology
Function and homology information


[ribosomal protein uS5]-alanine N-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups / cytoplasm
Similarity search - Function
: / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / [ribosomal protein uS5]-alanine N-acetyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsFavrot, L. / Hegde, S.S. / Blanchard, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI060899 United States
CitationJournal: To Be Published
Title: Structural Characterization of Mycobacterium smegmatis RimJ, an N-acetyltransferase protein
Authors: Favrot, L. / Hegde, S.S. / Blanchard, J.S.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyltransferase, GNAT family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8512
Polymers23,0411
Non-polymers8101
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-6 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.531, 63.531, 227.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

21A-549-

HOH

31A-593-

HOH

-
Components

#1: Protein Acetyltransferase, GNAT family protein


Mass: 23041.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5469 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R3G9
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate (pH 6.5), 20 % v/v 2-propanol and 20 % w/v polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.898→50 Å / Num. obs: 40630 / % possible obs: 99.4 % / Redundancy: 11.5 % / Net I/σ(I): 18.1
Reflection shellResolution: 1.898→2.01 Å / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 40630 / CC1/2: 0.84 / % possible all: 84

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.898→35.067 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 1126 4.99 %
Rwork0.1755 --
obs0.1771 40625 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→35.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 51 201 1873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071720
X-RAY DIFFRACTIONf_angle_d1.0032351
X-RAY DIFFRACTIONf_dihedral_angle_d11.143981
X-RAY DIFFRACTIONf_chiral_restr0.06251
X-RAY DIFFRACTIONf_plane_restr0.006297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8976-1.9450.30561450.2532742X-RAY DIFFRACTION99
1.945-1.99760.25821490.2172767X-RAY DIFFRACTION100
1.9976-2.05640.27961370.20842764X-RAY DIFFRACTION100
2.0564-2.12280.25851470.19972774X-RAY DIFFRACTION100
2.1228-2.19860.20061450.17742744X-RAY DIFFRACTION100
2.1986-2.28660.21051440.18292755X-RAY DIFFRACTION100
2.2866-2.39070.22311480.18232755X-RAY DIFFRACTION100
2.3907-2.51670.24181490.1862730X-RAY DIFFRACTION100
2.5167-2.67430.19811410.18582773X-RAY DIFFRACTION100
2.6743-2.88070.25821390.1882776X-RAY DIFFRACTION100
2.8807-3.17050.21871450.18472768X-RAY DIFFRACTION100
3.1705-3.62880.22051460.17552737X-RAY DIFFRACTION100
3.6288-4.57030.15961410.13772774X-RAY DIFFRACTION100
4.5703-35.07320.15611520.15892738X-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