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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 / Iron-sulfur
Function / homology
Function and homology information


apicoplast / : / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin, apicoplast
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
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.
History
DepositionMar 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: FERREDOXIN
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9556
Polymers22,5572
Non-polymers3984
Water8,935496
1
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5004
Polymers11,2781
Non-polymers2223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4542
Polymers11,2781
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP1211

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Components

#1: Protein FERREDOXIN


Mass: 11278.463 Da / Num. of mol.: 2 / Fragment: residues 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: pTrc99A / 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 / Source method: obtained synthetically / Formula: Na
#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.: 496 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 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 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2001
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→47.36 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.8
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2561 / % possible all: 97

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Processing

Software
NameClassification
d*TREKdata reduction
CNSrefinement
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 950538.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1247 5 %RANDOM
Rwork0.184 ---
all0.184 24864 --
obs0.184 24864 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.5155 Å2 / ksol: 0.36268 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å2-0.33 Å2
2--0.4 Å20 Å2
3----1.89 Å2
Refine analyzeLuzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 10 496 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
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 174 4.5 %
Rwork0.243 3677 -
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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