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- PDB-1rfs: RIESKE SOLUBLE FRAGMENT FROM SPINACH -

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Basic information

Entry
Database: PDB / ID: 1rfs
TitleRIESKE SOLUBLE FRAGMENT FROM SPINACH
ComponentsRIESKE PROTEIN
KeywordsIRON-SULFUR PROTEIN / ELECTRON TRANSPORT
Function / homology
Function and homology information


plastoquinol--plastocyanin reductase activity / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid membrane / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Cytochrome b6-f complex iron-sulfur subunit / 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 / Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsCarrell, C.J. / Zhang, H. / Cramer, W.A. / Smith, J.L.
Citation
Journal: Structure / Year: 1997
Title: Biological identity and diversity in photosynthesis and respiration: structure of the lumen-side domain of the chloroplast Rieske protein.
Authors: Carrell, C.J. / Zhang, H. / Cramer, W.A. / Smith, J.L.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Characterization and Crystallization of the Lumen Side Domain of the Chloroplast Rieske Iron-Sulfur Protein
Authors: Zhang, H. / Carrell, C.J. / Huang, D. / Sled, V. / Ohnishi, T. / Smith, J.L. / Cramer, W.A.
History
DepositionAug 14, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIESKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8122
Polymers14,6361
Non-polymers1761
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.050, 31.870, 35.790
Angle α, β, γ (deg.)95.60, 106.10, 117.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein RIESKE PROTEIN / / RIESKE IRON-SULFUR PROTEIN / RISP


Mass: 14636.430 Da / Num. of mol.: 1 / Fragment: SOLUBLE FRAGMENT, C-TERMINAL RESIDUES 41 - 179 / Source method: isolated from a natural source / Details: SUBUNIT OF THE CYTOCHROME B6-F COMPLEX / Source: (natural) Spinacia oleracea (spinach) / Organelle: CHLOROPLAST / Tissue: LEAF / References: UniProt: P08980
#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.: 143 / 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: 1.78 Å3/Da / Density % sol: 31 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate1reservoir
2100-200 mg/mlammonium acetate1reservoir
330 %PEG40001reservoir
450 mMsodium acetate1drop
550-100 mg/mlammonium acetate1drop
615 %PEG40001drop
715 mg/mlprotein1drop
810 mMMOPS1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 14, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. obs: 8758 / % possible obs: 89.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 10.1
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 6.5 / Rsym value: 0.108 / % possible all: 57.3
Reflection
*PLUS
Num. measured all: 28882
Reflection shell
*PLUS
% possible obs: 57.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22 391 4 %RANDOM
Rwork0.17 ---
obs0.17 8367 89.7 %-
Refinement stepCycle: LAST / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 4 143 1110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.92
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it10.3
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it11.4
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.83→1.87 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.251 30 4 %
Rwork0.244 469 -
obs--73.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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