[English] 日本語
Yorodumi
- PDB-2atw: Structure of a Mycobacterium tuberculosis NusA-RNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2atw
TitleStructure of a Mycobacterium tuberculosis NusA-RNA complex
Components
  • Transcription elongation protein nusA
  • ribosomal RNA (5'- AGAACUCAAUAG -3')
Keywordstranscription/RNA / Protein-RNA complex / transcription-RNA COMPLEX
Function / homology
Function and homology information


peptidoglycan-based cell wall / transcription antitermination / DNA-templated transcription termination / DNA-binding transcription factor activity / RNA binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / K homology (KH) domain / RNA-binding domain, S1 / Type-1 KH domain profile. ...Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / K homology (KH) domain / RNA-binding domain, S1 / Type-1 KH domain profile. / GMP Synthetase; Chain A, domain 3 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Nucleic acid-binding proteins / K homology domain superfamily, prokaryotic type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / K homology domain-like, alpha/beta / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Transcription termination/antitermination protein NusA / Transcription termination/antitermination protein NusA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBeuth, B. / Pennell, S. / Arnvig, K.B. / Martin, S.R. / Taylor, I.A.
CitationJournal: Embo J. / Year: 2005
Title: Structure of a Mycobacterium tuberculosis NusA-RNA complex.
Authors: Beuth, B. / Pennell, S. / Arnvig, K.B. / Martin, S.R. / Taylor, I.A.
History
DepositionAug 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: ribosomal RNA (5'- AGAACUCAAUAG -3')
D: ribosomal RNA (5'- AGAACUCAAUAG -3')
A: Transcription elongation protein nusA
C: Transcription elongation protein nusA


Theoretical massNumber of molelcules
Total (without water)61,7104
Polymers61,7104
Non-polymers00
Water3,747208
1
B: ribosomal RNA (5'- AGAACUCAAUAG -3')
A: Transcription elongation protein nusA


Theoretical massNumber of molelcules
Total (without water)30,8552
Polymers30,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: ribosomal RNA (5'- AGAACUCAAUAG -3')
C: Transcription elongation protein nusA


Theoretical massNumber of molelcules
Total (without water)30,8552
Polymers30,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.564, 89.543, 100.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsOne molecule NusA is in complex with one molecule RNA oligonucleotide. The biological assembly is a monomeric 1:1 complex. There are 2 biological assemblies in the asymmetric unit.

-
Components

#1: RNA chain ribosomal RNA (5'- AGAACUCAAUAG -3')


Mass: 3843.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide synthesis
#2: Protein Transcription elongation protein nusA


Mass: 27011.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: nusA / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A5M2, UniProt: P9WIV3*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.34 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, Potassium dihydrogenphosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→15 Å / Num. all: 28345 / Num. obs: 28167 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Rsym value: 0.078 / Net I/σ(I): 17.1
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2770 / Rsym value: 0.46 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ASB

2asb


Resolution: 2.25→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.301 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27267 1425 5.1 %RANDOM
Rwork0.20599 ---
all0.20934 26889 --
obs0.20934 26701 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.91 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.25→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 510 0 208 4083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213981
X-RAY DIFFRACTIONr_angle_refined_deg1.7342.1275505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2773446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.57115620
X-RAY DIFFRACTIONr_chiral_restr0.1040.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022838
X-RAY DIFFRACTIONr_nbd_refined0.2490.31679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5401
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.368
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.521
X-RAY DIFFRACTIONr_mcbond_it0.8951.52219
X-RAY DIFFRACTIONr_mcangle_it1.70423569
X-RAY DIFFRACTIONr_scbond_it2.5431762
X-RAY DIFFRACTIONr_scangle_it3.954.51936
LS refinement shellResolution: 2.25→2.307 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.381 107
Rwork0.251 1878

+
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