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- PDB-1rie: STRUCTURE OF A WATER SOLUBLE FRAGMENT OF THE RIESKE IRON-SULFUR P... -

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Basic information

Entry
Database: PDB / ID: 1rie
TitleSTRUCTURE OF A WATER SOLUBLE FRAGMENT OF THE RIESKE IRON-SULFUR PROTEIN OF THE BOVINE HEART MITOCHONDRIAL CYTOCHROME BC1-COMPLEX
ComponentsRIESKE IRON-SULFUR PROTEIN
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / HISTIDINE LIGANDS / RIESKE IRON-SULFUR CLUSTER
Function / homology
Function and homology information


Complex III assembly / Respiratory electron transport / respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / mitochondrion / metal ion binding
Similarity search - Function
Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 3-layer Sandwich / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome c reductase, iron-sulphur subunit ...Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 3-layer Sandwich / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / 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 / Cytochrome b-c1 complex subunit Rieske, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsIwata, S. / Saynovits, M. / Link, T.A. / Michel, H.
Citation
Journal: Structure / Year: 1996
Title: Structure of a water soluble fragment of the 'Rieske' iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 A resolution.
Authors: Iwata, S. / Saynovits, M. / Link, T.A. / Michel, H.
#1: Journal: Eur.J.Biochem. / Year: 1996
Title: Isolation, Characterisation and Crystallisation of a Water-Soluble Fragment of the Rieske Iron-Sulfur Protein of Bovine Heart Mitochondrial Bc1 Complex
Authors: Link, T.A. / Saynovits, M. / Assmann, C. / Iwata, S. / Ohnishi, T. / Von Jagow, G.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: The Mitochondrial Targeting Presequence of the Rieske Iron-Sulfur Protein is Processed in a Single Step After Insertion Into the Cytochrome Bc1 Complex in Mammals and Retained as a Subunit in the Complex
Authors: Brandt, U. / Yu, L. / Yu, C.A. / Trumpower, B.L.
#3: Journal: Biochem.Biophys.Res.Commun. / Year: 1990
Title: Cloning and Sequencing of a Cdna Encoding the Rieske Iron-Sulfur Protein of Bovine Heart Mitochondrial Ubiquinol-Cytochrome C Reductase
Authors: Usui, S. / Yu, L. / Yu, C.A.
#4: Journal: FEBS Lett. / Year: 1987
Title: Isolation and Amino Acid Sequence of the 'Rieske' Iron Sulfur Protein of Beef Heart Ubiquinol:Cytochrome C Reductase
Authors: Schagger, H. / Borchart, U. / Machleidt, W. / Link, T.A. / Von Jagow, G.
History
DepositionFeb 23, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6162
Polymers14,4411
Non-polymers1761
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.100, 53.000, 38.000
Angle α, β, γ (deg.)90.00, 100.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RIESKE IRON-SULFUR PROTEIN / UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR


Mass: 14440.658 Da / Num. of mol.: 1 / Fragment: SOLUBLE FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: P13272, quinol-cytochrome-c reductase
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.2 Å3/Da / Density % sol: 41 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5-3 mg/mlprotein1drop
22 mM1dropNa2S2O4
320-30 %PEG60001reservoir
4100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 10, 1995
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 18058 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 3.52 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.6
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.5 / % possible all: 68
Reflection
*PLUS
Num. measured all: 63633
Reflection shell
*PLUS
% possible obs: 68 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.211 -5 %
Rwork0.187 --
obs0.187 15165 75.6 %
Displacement parametersBiso mean: 9.21 Å2
Refine analyzeLuzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 4 167 1340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.324
X-RAY DIFFRACTIONx_mcangle_it2.949
X-RAY DIFFRACTIONx_scbond_it2.553
X-RAY DIFFRACTIONx_scangle_it3.188
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 15880 / Rfactor all: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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