[English] 日本語
Yorodumi
- PDB-4l4u: Crystal structure of construct containing A. aeolicus NtrC1 recei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l4u
TitleCrystal structure of construct containing A. aeolicus NtrC1 receiver, central and DNA binding domains
ComponentsTranscriptional regulator (NtrC family)
KeywordsPROTEIN BINDING / Receiver domain / AAA+ ATPase domain / Transcriptional initiation / ATP binding
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator (NtrC family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVidangos, N.K. / Maris, A.E. / Young, A. / Hong, E. / Pelton, J.G. / Batchelor, J.D. / Wemmer, D.E.
CitationJournal: Biopolymers / Year: 2013
Title: Structure, function, and tethering of DNA-binding domains in sigma (54) transcriptional activators.
Authors: Vidangos, N. / Maris, A.E. / Young, A. / Hong, E. / Pelton, J.G. / Batchelor, J.D. / Wemmer, D.E.
History
DepositionJun 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator (NtrC family)


Theoretical massNumber of molelcules
Total (without water)51,2301
Polymers51,2301
Non-polymers00
Water2,846158
1
A: Transcriptional regulator (NtrC family)

A: Transcriptional regulator (NtrC family)


Theoretical massNumber of molelcules
Total (without water)102,4592
Polymers102,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y,-z+5/21
Buried area9360 Å2
ΔGint-13 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.421, 107.010, 98.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

21A-599-

HOH

-
Components

#1: Protein Transcriptional regulator (NtrC family)


Mass: 51229.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: ntrC1, aq_1117 / Production host: Escherichia coli (E. coli) / References: UniProt: O67198
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.15 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→19.8 Å / Num. all: 27687 / Num. obs: 27022 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.8 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1313 4.86 %RANDOM
Rwork0.2129 ---
obs0.2147 27021 97.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.614 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.0431 Å20 Å2-0 Å2
2--7.2439 Å20 Å2
3----0.2008 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 0 158 3273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033169
X-RAY DIFFRACTIONf_angle_d0.6964247
X-RAY DIFFRACTIONf_dihedral_angle_d15.0051239
X-RAY DIFFRACTIONf_chiral_restr0.04478
X-RAY DIFFRACTIONf_plane_restr0.002539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2880.27551470.26562742X-RAY DIFFRACTION95
2.288-2.3920.2521500.24932787X-RAY DIFFRACTION96
2.392-2.51790.291300.2482817X-RAY DIFFRACTION97
2.5179-2.67530.2621520.24842844X-RAY DIFFRACTION98
2.6753-2.88130.28741480.24922827X-RAY DIFFRACTION98
2.8813-3.17020.28311690.22772851X-RAY DIFFRACTION98
3.1702-3.62650.23461370.20892901X-RAY DIFFRACTION99
3.6265-4.55980.22531260.17932941X-RAY DIFFRACTION99
4.5598-19.83830.231540.19932998X-RAY DIFFRACTION98

+
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://pdbjlvh1.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