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- PDB-1iue: Crystal Structure Analysis of ferredoxin from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 1iue
TitleCrystal Structure Analysis of ferredoxin from Plasmodium falciparum
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / Electron transport / Iron-sulfur
Function / homology2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / apicoplast / 2 iron, 2 sulfur cluster binding ...2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / apicoplast / 2 iron, 2 sulfur cluster binding / oxidation-reduction process / electron transfer activity / metal ion binding / Ferredoxin, apicoplast
Function and homology information
Specimen sourcePlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.7 Å resolution
AuthorsKimata-Ariga, Y. / Kurisu, G. / Hase, T.
CitationJournal: To be Published
Title: Redox power generator of a nonphotosynthetic plastid in malaria parasite
Authors: Kimata-Ariga, Y. / Kurisu, G. / Hase, T.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 4, 2002 / Release: Sep 30, 2003
RevisionDateData content typeGroupCategoryProviderType
1.0Sep 30, 2003Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: FERREDOXIN
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9556
Polyers22,5572
Non-polymers3984
Water8,935496
1
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5004
Polyers11,2781
Non-polymers2223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4542
Polyers11,2781
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)49.000, 50.573, 52.480
Angle α, β, γ (deg.)90.00, 115.53, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide FERREDOXIN /


Mass: 11278.463 Da / Num. of mol.: 2 / Fragment: residues 1-98
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Genus: Plasmodium / Species: Plasmodium falciparum / Strain: 3D7 / Plasmid name: pTrc99A / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: Q8IED5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Formula: Na / Sodium
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 496 / Formula: H2O / Water

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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: 2.6 / Density percent sol: 52.71 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, sodium acetate trihydrate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Collection date: Sep 1, 2001
RadiationMonochromator: OSMIC MIRROR / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 11.4 Å2 / D resolution high: 1.7 Å / D resolution low: 47.36 Å / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.085 / NetI over sigmaI: 14.8 / Redundancy: 3.48 %
Reflection shellRmerge I obs: 0.187 / Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / MeanI over sigI obs: 4.2 / Number unique all: 2561 / Percent possible all: 97

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Processing

Software
NameClassification
d*TREKdata reduction
CNSrefinement
d*TREKdata scaling
CNSphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / R Free selection details: RANDOM / Data cutoff high absF: 950538.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 33.5155 / Solvent model param ksol: 0.36268
Displacement parametersB iso mean: 14.8 Å2 / Aniso B11: 1.5 Å2 / Aniso B12: 0 Å2 / Aniso B13: -0.33 Å2 / Aniso B22: 0.4 Å2 / Aniso B23: 0 Å2 / Aniso B33: -1.89 Å2
Least-squares processR factor R free: 0.221 / R factor R free error: 0.006 / R factor R work: 0.184 / R factor all: 0.184 / R factor obs: 0.184 / Highest resolution: 1.7 Å / Lowest resolution: 47.36 Å / Number reflection R free: 1247 / Number reflection all: 24864 / Number reflection obs: 24864 / Percent reflection R free: 5 / Percent reflection obs: 96.8
Refine analyzeLuzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.12 Å
Refine hist #LASTHighest resolution: 1.7 Å / Lowest resolution: 47.36 Å
Number of atoms included #LASTProtein: 1568 / Nucleic acid: 0 / Ligand: 10 / Solvent: 496 / Total: 2074
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.73
Refine LS shellHighest resolution: 1.7 Å / R factor R free: 0.278 / R factor R free error: 0.021 / R factor R work: 0.243 / Lowest resolution: 1.81 Å / Number reflection R free: 174 / Number reflection R work: 3677 / Total number of bins used: 6 / Percent reflection R free: 4.5 / Percent reflection obs: 90.1
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FES.PARAMFES.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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