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- PDB-1nyk: Crystal Structure of the Rieske protein from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1nyk
TitleCrystal Structure of the Rieske protein from Thermus thermophilus
ComponentsRieske iron-sulfur protein
KeywordsELECTRON TRANSPORT / beta barrel / Iron Sulfur cluster
Function / homology
Function and homology information


: / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / metal ion binding / plasma 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] 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
FE2/S2 (INORGANIC) CLUSTER / Rieske iron-sulfur protein / Quinol-cytochrome c reductase, Rieske iron-sulfur subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.31 Å
AuthorsHunsicker-Wang, L.M. / Heine, A. / Chen, Y. / Luna, E.P. / Todaro, T. / Zhang, Y.M. / Williams, P.A. / McRee, D.E. / Hirst, J. / Stout, C.D. / Fee, J.A.
CitationJournal: Biochemistry / Year: 2003
Title: High resolution structure of the soluble, respiratory-type Rieske protein from Thermus thermophilus: Analysis and Comparison
Authors: Hunsicker-Wang, L.M. / Heine, A. / Chen, Y. / Luna, E.P. / Todaro, T. / Zhang, Y.M. / Williams, P.A. / McRee, D.E. / Hirst, J. / Stout, C.D. / Fee, J.A.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999AUTHORS STATED THAT RESIDUE ARG 173 OF THE DEPOSITED SEQUENCE IS CORRECT AND THAT THE GENBANK ...AUTHORS STATED THAT RESIDUE ARG 173 OF THE DEPOSITED SEQUENCE IS CORRECT AND THAT THE GENBANK SEQUENCE IS IN ERROR AT THIS POSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rieske iron-sulfur protein
B: Rieske iron-sulfur protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2767
Polymers34,8522
Non-polymers4255
Water6,323351
1
A: Rieske iron-sulfur protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6755
Polymers17,4261
Non-polymers2494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rieske iron-sulfur protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6022
Polymers17,4261
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.569, 78.267, 136.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1234-

HOH

21A-1250-

HOH

31A-1261-

HOH

41A-1278-

HOH

51A-1286-

HOH

61B-1326-

HOH

71B-1334-

HOH

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Components

#1: Protein Rieske iron-sulfur protein


Mass: 17425.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): DH10 / References: UniProt: O52396, UniProt: Q5SGZ9*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Peg 4000, Tris, magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 %PEG40001reservoir
3100 mMTris1reservoirpH8.5
40.1-0.4 M1reservoirMgCl2
51reservoir10000-11000nmH2O

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211.7373, 1.3776, 1.7415
SYNCHROTRONSSRL BL7-120.965
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2001 / Details: Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorMADMx-ray1
2single crystal Si(111) bent monochromator (horizontal focusing)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.73731
21.37761
31.74151
40.9651
ReflectionResolution: 1.3→24 Å / Num. obs: 74518 / % possible obs: 98.8 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.7 / Redundancy: 4.2 %
Reflection shellResolution: 1.31→1.37 Å / % possible all: 90.4
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 50 Å / Num. obs: 76407 / Num. measured all: 319817 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.3 Å / % possible obs: 93.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.31→24 Å / Num. parameters: 23819 / Num. restraintsaints: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3%
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 3722 5.3 %RANDOM
Rwork0.1576 ---
all0.1592 74518 --
obs0.1592 74518 93.4 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2301 / Occupancy sum non hydrogen: 2668.5
Refinement stepCycle: LAST / Resolution: 1.31→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 11 351 2672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.189 / Rfactor Rwork: 0.137
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.28
LS refinement shell
*PLUS
Rfactor Rfree: 0.212 / Rfactor Rwork: 0.158

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