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- PDB-3fou: Low pH structure of the Rieske protein from Thermus thermophilus ... -

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Basic information

Entry
Database: PDB / ID: 3fou
TitleLow pH structure of the Rieske protein from Thermus thermophilus at 2.1 A
ComponentsQuinol-cytochrome c reductase, Rieske iron-sulfur subunit
KeywordsELECTRON TRANSPORT / Rieske protein / Pr / [2Fe-2S]
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / intracellular membrane-bounded organelle / metal ion binding / plasma membrane / cytoplasm
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] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FE2/S2 (INORGANIC) CLUSTER / PRASEODYMIUM ION / Quinol-cytochrome c reductase, Rieske iron-sulfur subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHunsicker-Wang, L.M. / Taylor, A.B.
CitationJournal: Biochemistry / Year: 2009
Title: Effects of pH on the Rieske Protein from Thermus thermophilus: A Spectroscopic and Structural Analysis
Authors: Konkle, M.E. / Muellner, S.K. / Schwander, A.L. / Dicus, M.M. / Pokhrel, R. / Britt, R.D. / Taylor, A.B. / Hunsicker-Wang, L.M.
History
DepositionJan 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Quinol-cytochrome c reductase, Rieske iron-sulfur subunit
B: Quinol-cytochrome c reductase, Rieske iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,26114
Polymers32,8662
Non-polymers1,39512
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-75 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.152, 58.512, 58.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Quinol-cytochrome c reductase, Rieske iron-sulfur subunit


Mass: 16432.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1931 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SGZ9

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Non-polymers , 5 types, 126 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Pr
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.21
Details: PEG 8000, Na Cacodylate, Calcium acetate, Pr(acetate)3, pH 6.21, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 11, 2008 / Details: Mirrors
RadiationMonochromator: Confocal multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→58.8 Å / Num. obs: 23456 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rsym value: 0.088
Reflection shellResolution: 2.099→2.154 Å / Redundancy: 4.4 % / Num. unique all: 2311 / Rsym value: 0.529 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Protein A of 1NYK

1nyk


Resolution: 2.1→58.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.985 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24601 1205 5.1 %RANDOM
Rwork0.19806 ---
all0.20072 23456 --
obs0.20072 22217 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.758 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 24 114 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222412
X-RAY DIFFRACTIONr_angle_refined_deg1.8622.0093300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26625.10694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69315363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6991511
X-RAY DIFFRACTIONr_chiral_restr0.1170.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021873
X-RAY DIFFRACTIONr_nbd_refined0.2190.21075
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2162
X-RAY DIFFRACTIONr_metal_ion_refined0.4360.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.25
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0720.21
X-RAY DIFFRACTIONr_mcbond_it1.0791.51615
X-RAY DIFFRACTIONr_mcangle_it1.75922548
X-RAY DIFFRACTIONr_scbond_it2.6233883
X-RAY DIFFRACTIONr_scangle_it4.1664.5748
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 88 -
Rwork0.238 1591 -
obs--98.65 %

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