[English] 日本語
Yorodumi
- PDB-1jm1: Crystal structure of the soluble domain of the Rieske protein II ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jm1
TitleCrystal structure of the soluble domain of the Rieske protein II (soxF) from Sulfolobus acidocaldarius
ComponentsRieske iron-sulfur protein soxF
Keywordselectron transport / oxidoreductase / Rieske iron-sulfur protein / respiratory chain
Function / homology
Function and homology information


: / 2 iron, 2 sulfur cluster binding / membrane / metal ion binding
Similarity search - Function
Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Rieske (2Fe-2S) protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.11 Å
AuthorsBoenisch, H. / Schmidt, C.L. / Schaefer, G. / Ladenstein, R.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution.
Authors: Bonisch, H. / Schmidt, C.L. / Schafer, G. / Ladenstein, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary crystallographic analysis of Rieske iron-sulfur protein II (soxF) from Sulfolobus acidocaldarius
Authors: Boenisch, H. / Schmidt, C.L. / Schaefer, G. / Ladenstein, R.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1997
Title: Expression of the Sulfolobus acidocaldarius Rieske iron sulfur protein II (soxF) with the correctly inserted [2Fe-2S] cluster in Escherichia coli
Authors: Schmidt, C.L. / Hatzfeld, O.M. / Petersen, A. / Link, T.A. / Schaefer, G.
History
DepositionJul 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rieske iron-sulfur protein soxF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8993
Polymers21,6991
Non-polymers2002
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.252, 80.252, 75.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

-
Components

#1: Protein Rieske iron-sulfur protein soxF / Rieske protein / soxF / Quinol oxidase-2


Mass: 21699.285 Da / Num. of mol.: 1 / Fragment: Soluble domain, C-terminal residues 47 - 250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: SOXF / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q53766
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, magnesium acetate, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, at 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 29, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.11→20 Å / Num. all: 112015 / Num. obs: 109985 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.2 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 32.4
Reflection shellResolution: 1.11→1.13 Å / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4935 / % possible all: 73.6
Reflection
*PLUS
Lowest resolution: 69 Å / Num. obs: 112015 / Num. measured all: 2039387 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 73.6 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.11→20 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1247 5409 4.9 %RANDOM
Rwork0.1063 ---
all0.1063 112015 --
obs0.1063 109985 98.2 %-
Displacement parametersBiso mean: 19.64 Å2
Refinement stepCycle: LAST / Resolution: 1.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 5 298 3460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.124
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.166
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 69 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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