[English] 日本語
Yorodumi
- PDB-1m1h: Crystal structure of Aquifex aeolicus N-utilization substance G (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m1h
TitleCrystal structure of Aquifex aeolicus N-utilization substance G (NusG), Space group I222
ComponentsTranscription antitermination protein nusG
KeywordsTRANSCRIPTION / Transcription termination / Antitermination / RNP motif / immunoglobulin fold / nucleic acid interaction / protein-protein interaction
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / cytosol
Similarity search - Function
N-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / NusG, N-terminal domain / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. ...N-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / NusG, N-terminal domain / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Alpha-Beta Plaits / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsSteiner, T. / Kaiser, J.T. / Marinkovic, S. / Huber, R. / Wahl, M.C.
CitationJournal: Embo J. / Year: 2002
Title: Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities
Authors: Steiner, T. / Kaiser, J.T. / Marinkovic, S. / Huber, R. / Wahl, M.C.
History
DepositionJun 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)28,0421
Polymers28,0421
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.1, 86.2, 108.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a monomer

-
Components

#1: Protein Transcription antitermination protein nusG


Mass: 28041.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67757
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 4000, 2-Propanol, Sodium Chloride, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MMES/Tris1reservoirpH5.8
210 %PEG40001reservoir
320 %2-propanol1reservoir
40.1 M1reservoirNaCl
520 mMTris-HCl1droppH7.0
650 mM1dropNaCl
71 MDNA1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: CCD / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 27602 / Num. obs: 27602 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rsym value: 0.074 / Net I/σ(I): 30
Reflection shellResolution: 1.95→2.05 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.504 / % possible all: 98.4
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.504

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
REFMACrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.95→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1380 -random
Rwork0.234 ---
all0.234 27602 --
obs0.234 27602 98.4 %-
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 0 296 1732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.42
X-RAY DIFFRACTIONo_bond_d0.006
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / Rfactor Rwork: 0.283

+
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