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- PDB-2num: Soluble domain of Rieske Iron-Sulfur Protein -

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Basic information

Entry
Database: PDB / ID: 2num
TitleSoluble domain of Rieske Iron-Sulfur Protein
ComponentsUbiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Iron sulfur cluster
Function / homology
Function and homology information


quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / 2 iron, 2 sulfur cluster binding / intracellular membrane-bounded organelle / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ubiquinol-cytochrome c reductase iron-sulfur subunit
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.5 Å
AuthorsKolling, D. / Brunzelle, J. / Lhee, S. / Crofts, A.R. / Nair, S.K.
CitationJournal: Structure / Year: 2007
Title: Atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters.
Authors: Kolling, D.J. / Brunzelle, J.S. / Lhee, S. / Crofts, A.R. / Nair, S.K.
History
DepositionNov 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3222
Polymers15,1461
Non-polymers1761
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.626, 70.626, 54.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 15146.142 Da / Num. of mol.: 1 / Fragment: residues 47-187 / Mutation: Y156F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petA, fbcF / Production host: Escherichia coli (E. coli) / References: UniProt: Q02762, quinol-cytochrome-c reductase
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.5 M ammonium sulfate, 20% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→18 Å / Num. obs: 19979 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 5.1
Reflection shellResolution: 1.5→1.61 Å / Redundancy: 14 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 15 / Num. unique all: 1938 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.865 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16726 1567 7.3 %RANDOM
Rwork0.15249 ---
obs0.15357 19979 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.355 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 4 113 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221089
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.951479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55223.95848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.71715168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.673158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02837
X-RAY DIFFRACTIONr_nbd_refined0.1950.2452
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0720.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.215
X-RAY DIFFRACTIONr_mcbond_it0.8321.5715
X-RAY DIFFRACTIONr_mcangle_it1.29421115
X-RAY DIFFRACTIONr_scbond_it1.8313423
X-RAY DIFFRACTIONr_scangle_it2.7994.5362
LS refinement shellResolution: 1.5→1.581 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.181 220 -
Rwork0.131 2837 -
obs--97.89 %

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