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- PDB-2nuk: Soluble Domain of the Rieske Iron-Sulfur Protein from Rhodobacter... -

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Basic information

Entry
Database: PDB / ID: 2nuk
TitleSoluble Domain of the Rieske Iron-Sulfur Protein from Rhodobacter sphaeroides
ComponentsUbiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Iron Sulfur CLuster
Function / homology
Function and homology information


quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / 2 iron, 2 sulfur cluster binding / metal ion binding / plasma membrane
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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] 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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 1.0Apr 10, 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 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,3382
Polymers15,1621
Non-polymers1761
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.568, 70.568, 54.769
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: 15162.142 Da / Num. of mol.: 1 / Fragment: residues 47-187
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


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.: 198 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.5 M Ammonium sulfate, 20% anhydrous glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→12 Å / Num. all: 41254 / Num. obs: 41254 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 24.7
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 19.6 / Num. unique all: 4192 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NWF

2nwf


Resolution: 1.2→11.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.669 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13639 3177 7.7 %RANDOM
Rwork0.11828 ---
obs0.11969 38022 98.16 %-
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: 9.781 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.2→11.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 4 198 2355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0221121
X-RAY DIFFRACTIONr_bond_other_d0.0010.021013
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9531530
X-RAY DIFFRACTIONr_angle_other_deg0.95332354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0895148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50323.95848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.53215173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.87158
X-RAY DIFFRACTIONr_chiral_restr0.090.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021294
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02227
X-RAY DIFFRACTIONr_nbd_refined0.2310.3203
X-RAY DIFFRACTIONr_nbd_other0.1920.31099
X-RAY DIFFRACTIONr_nbtor_refined0.170.5567
X-RAY DIFFRACTIONr_nbtor_other0.0830.5646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.5217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.34
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1220.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.539
X-RAY DIFFRACTIONr_mcbond_it1.1451.5926
X-RAY DIFFRACTIONr_mcbond_other0.5331.5301
X-RAY DIFFRACTIONr_mcangle_it1.51331162
X-RAY DIFFRACTIONr_scbond_it1.3632459
X-RAY DIFFRACTIONr_scangle_it1.8693366
X-RAY DIFFRACTIONr_rigid_bond_restr0.74721379
X-RAY DIFFRACTIONr_sphericity_free21.20130198
X-RAY DIFFRACTIONr_sphericity_bonded2.547301092
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.113 235 -
Rwork0.102 2803 -
obs--99.64 %

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