[English] 日本語
Yorodumi
- PDB-1ku7: Crystal Structure of Thermus aquatics RNA Polymerase SigmaA Subun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ku7
TitleCrystal Structure of Thermus aquatics RNA Polymerase SigmaA Subunit Region 4 Bound to-35 Element DNA
Components
  • 5'-D(*CP*CP*TP*TP*GP*AP*CP*AP*AP*AP*G)-3'
  • 5'-D(*CP*CP*TP*TP*TP*GP*TP*CP*AP*AP*G)-3'
  • sigma factor sigA
KeywordsTRANSCRIPTION/DNA / helix-turn-helix / double-helix / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
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 ...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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCampbell, E.A. / Muzzin, O. / Chlenov, M. / Sun, J.L. / Olson, C.A. / Weinman, O. / Trester-Zedlitz, M.L. / Darst, S.A.
CitationJournal: Mol.Cell / Year: 2002
Title: Structure of the bacterial RNA polymerase promoter specificity sigma subunit.
Authors: Campbell, E.A. / Muzzin, O. / Chlenov, M. / Sun, J.L. / Olson, C.A. / Weinman, O. / Trester-Zedlitz, M.L. / Darst, S.A.
History
DepositionJan 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(*CP*CP*TP*TP*GP*AP*CP*AP*AP*AP*G)-3'
C: 5'-D(*CP*CP*TP*TP*TP*GP*TP*CP*AP*AP*G)-3'
A: sigma factor sigA
D: sigma factor sigA


Theoretical massNumber of molelcules
Total (without water)24,1414
Polymers24,1414
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.180, 62.650, 94.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: DNA chain 5'-D(*CP*CP*TP*TP*GP*AP*CP*AP*AP*AP*G)-3'


Mass: 3342.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: -35 Element DNA
#2: DNA chain 5'-D(*CP*CP*TP*TP*TP*GP*TP*CP*AP*AP*G)-3'


Mass: 3324.184 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein sigma factor sigA


Mass: 8737.127 Da / Num. of mol.: 2 / Fragment: region 4 (residues 366-438) / Mutation: L386M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EZJ8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MES, PEG 4000, magnesium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2PEG 400011
3magnesium acetate11
Crystal grow
*PLUS
Temperature: 22.5 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
20.1 MMES1reservoirpH6.0
32.4 Mammonium sulfate1reservoir
420 mM1reservoirMgCl2

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 9, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 8898 / Num. obs: 8698 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 %
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2.9 / % possible all: 79.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 25 Å / Num. obs: 7801 / Num. measured all: 29108 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.3

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→25 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.293 484 -
Rwork0.255 --
all0.255 8898 -
obs0.255 8698 97.8 %
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 442 0 67 1645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00696
X-RAY DIFFRACTIONc_angle_deg1.3
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00696
X-RAY DIFFRACTIONc_angle_deg1.3

+
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