[English] 日本語
Yorodumi
- PDB-9fjl: Sulfolobus acidocaldarius NusA2 structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fjl
TitleSulfolobus acidocaldarius NusA2 structure
ComponentsTranscription elongation factor NusA
KeywordsUNKNOWN FUNCTION / crenarchaea / zinc finger domain
Function / homologytranslation elongation factor activity / Transcription elongation factor NusA
Function and homology information
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPilotto, S. / Phung, D.K. / Pinotsis, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust207446/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: Structure, function and evolution of crenarchaeal NusA2
Authors: Phung, D.K. / Pilotto, S. / Matelska, D. / Pinotsis, N. / Werner, F.
History
DepositionMay 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription elongation factor NusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2832
Polymers19,2171
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, No evidences it forms oligomers.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.691, 118.691, 77.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Transcription elongation factor NusA


Mass: 19217.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein was cloned from Sulfolobus acidocaldarius genome and expressed full-length without any tag.
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: ATY89_02565, ATZ20_05595 / Plasmid: pET21a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A0U2WS94
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 8.39 Å3/Da / Density % sol: 85.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.9M sodium di-hydrogen phosphate/potassium di-hydrogen phosphate, 100mM Hepes pH 7.0 5mg/ml sample concentration

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.1→62.11 Å / Num. obs: 11814 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.036 / Rrim(I) all: 0.124 / Χ2: 0.68 / Net I/σ(I): 16.2
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 12 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2124 / CC1/2: 0.82 / Rpim(I) all: 0.267 / Rrim(I) all: 0.378 / Χ2: 0.19 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASER2.8.2phasing
AimlessCCP4 v8.0.012data scaling
xia2CCP4 v8.0.012data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→51.39 Å / SU ML: 0.3016 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.9006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 595 5.04 %
Rwork0.22 11204 -
obs0.2213 11799 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.39 Å2
Refinement stepCycle: LAST / Resolution: 3.1→51.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 1 0 1349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01081365
X-RAY DIFFRACTIONf_angle_d1.35061840
X-RAY DIFFRACTIONf_chiral_restr0.0743221
X-RAY DIFFRACTIONf_plane_restr0.0109228
X-RAY DIFFRACTIONf_dihedral_angle_d8.2091182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.410.39371630.35772733X-RAY DIFFRACTION99.97
3.41-3.910.26511420.26262777X-RAY DIFFRACTION99.97
3.91-4.920.29821480.22092797X-RAY DIFFRACTION100
4.92-51.390.18041420.18252897X-RAY DIFFRACTION99.93

+
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