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- PDB-1jm1: Crystal structure of the soluble domain of the Rieske protein II ... -

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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 / homologyRieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulphur domain superfamily / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / oxidoreductase activity, acting on diphenols and related substances as donors / 2 iron, 2 sulfur cluster binding / membrane / metal ion binding / Rieske (2Fe-2S) protein
Function and homology information
Specimen sourceSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 1.11 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 17, 2001 / Release: Jul 17, 2002
RevisionDateData content typeGroupProviderType
1.0Jul 17, 2002Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,8993
Polyers21,6991
Non-polymers2002
Water5,134285
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 61

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Components

#1: Protein/peptide 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: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Genus: Sulfolobus / Gene: SOXF / Plasmid name: pET3A / Genus (production host): Escherichia / 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 / Formula: Mg / Magnesium
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 285 / Formula: H2O / Water

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.24 / Density percent sol: 62 %
Crystal growTemp: 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
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
110 %(w/v)PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Collection date: Oct 29, 1999
RadiationDiffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 12.2 Å2 / D resolution high: 1.11 Å / D resolution low: 2 Å / Number all: 112015 / Number obs: 109985 / Observed criterion sigma F: 0 / Observed criterion sigma I: -3 / Rmerge I obs: 0.046 / NetI over sigmaI: 32.4 / Redundancy: 18.2 % / Percent possible obs: 98.2
Reflection shellRmerge I obs: 0.275 / Highest resolution: 1.11 Å / Lowest resolution: 1.13 Å / MeanI over sigI obs: 3.8 / Number unique all: 4935 / Percent possible all: 73.6
Reflection
*PLUS
D resolution low: 69 Å / Number obs: 112015 / Number measured all: 2039387 / Rmerge I obs: 0.047
Reflection shell
*PLUS
Percent possible obs: 73.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement
RefineMethod to determine structure: MAD / R Free selection details: RANDOM / Cross valid method: FREE R / Sigma F: 0 / Stereochemistry target values: ENGH & HUBER
Displacement parametersB iso mean: 19.64 Å2
Least-squares processR factor R free: 0.1247 / R factor R work: 0.1063 / R factor all: 0.1063 / R factor obs: 0.1063 / Highest resolution: 1.11 Å / Lowest resolution: 2 Å / Number reflection R free: 5409 / Number reflection all: 112015 / Number reflection obs: 109985 / Percent reflection R free: 4.9 / Percent reflection obs: 98.2
Refine hist #LASTHighest resolution: 1.11 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 3157 / Nucleic acid: 0 / Ligand: 5 / Solvent: 298 / Total: 3460
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.020
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
Least-squares process
*PLUS
Lowest resolution: 69 Å

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