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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 / homology
Function and homology information


2 iron, 2 sulfur cluster binding / metal ion binding / membrane
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] domain / Rieske [2Fe-2S] iron-sulphur 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
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 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

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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 %

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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

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