[English] 日本語
Yorodumi
- PDB-4x8k: Mycobacterium tuberculosis RbpA-SID in complex with SigmaA domain 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x8k
TitleMycobacterium tuberculosis RbpA-SID in complex with SigmaA domain 2
Components
  • RNA polymerase sigma factor SigA
  • RNA polymerase-binding protein RbpA
KeywordsTRANSCRIPTION ACTIVATOR / Sigma factor
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / response to water / bacterial-type RNA polymerase core enzyme binding / sigma factor activity / peptidoglycan-based cell wall / DNA-templated transcription initiation / nucleic acid binding / positive regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm
Similarity search - Function
RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 ...RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor SigA / RNA polymerase sigma factor SigA / RNA polymerase-binding protein RbpA / RNA polymerase-binding protein RbpA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.202 Å
AuthorsHubin, E.A. / Flack, J.E. / Tabib-Salazar, A. / Paget, M.S. / Darst, S.A. / Campbell, E.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA.
Authors: Hubin, E.A. / Tabib-Salazar, A. / Humphrey, L.J. / Flack, J.E. / Olinares, P.D. / Darst, S.A. / Campbell, E.A. / Paget, M.S.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA polymerase sigma factor SigA
B: RNA polymerase-binding protein RbpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6426
Polymers25,2922
Non-polymers3504
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-40 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.459, 84.459, 73.701
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

-
Components

#1: Protein RNA polymerase sigma factor SigA / Sigma-A


Mass: 14789.088 Da / Num. of mol.: 1 / Fragment: Domain 2 (UNP residues 236-364)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: sigA, mysA, rpoD, rpoV, MT2777 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGI0, UniProt: P9WGI1*PLUS
#2: Protein RNA polymerase-binding protein RbpA


Mass: 10502.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rbpA, MT2110 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WHJ4, UniProt: P9WHJ5*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.5, 0.5M ammonium sulfate

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.74 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. obs: 29225 / % possible obs: 98 % / Redundancy: 4.9 % / Biso Wilson estimate: 41.81 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.048 / Rrim(I) all: 0.109 / Χ2: 1.819 / Net I/av σ(I): 22.355 / Net I/σ(I): 9.5 / Num. measured all: 144080
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.283.10.57825280.7710.3370.6740.77283.9
2.28-2.373.70.5228510.8550.2930.60.76396.7
2.37-2.484.50.50529870.8930.2650.5720.80999.9
2.48-2.615.20.38529760.9420.1860.4280.86100
2.61-2.775.40.30129420.9670.1430.3330.947100
2.77-2.995.50.18829980.9860.0890.2081.195100
2.99-3.295.50.14429920.9890.0680.1591.684100
3.29-3.765.40.09529780.9940.0450.1052.869100
3.76-4.745.30.06829760.9960.0330.0763.551100
4.74-455.40.05829970.9970.0280.0643.496100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1839)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KU2, Chain A, Residues 204-268

1ku2


Resolution: 2.202→42.229 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1454 5.01 %
Rwork0.195 27547 -
obs0.1968 29001 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.01 Å2 / Biso mean: 57.1612 Å2 / Biso min: 26.62 Å2
Refinement stepCycle: final / Resolution: 2.202→42.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 25 58 1337
Biso mean--94.06 56.89 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051295
X-RAY DIFFRACTIONf_angle_d0.7011741
X-RAY DIFFRACTIONf_chiral_restr0.024188
X-RAY DIFFRACTIONf_plane_restr0.002220
X-RAY DIFFRACTIONf_dihedral_angle_d15.575496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2022-2.28090.29681280.28642255238379
2.2809-2.37220.34491400.25922668280895
2.3722-2.48010.2881430.24828402983100
2.4801-2.61090.27661380.223728252963100
2.6109-2.77440.25371650.222727822947100
2.7744-2.98860.27921740.217528172991100
2.9886-3.28920.25671720.219428192991100
3.2892-3.7650.20081420.186128342976100
3.765-4.74240.19691260.154328432969100
4.7424-42.23720.20171260.182328642990100

+
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