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- PDB-2ok8: Ferredoxin-NADP+ reductase from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 2ok8
TitleFerredoxin-NADP+ reductase from Plasmodium falciparum
ComponentsPutative ferredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / disulfide-stabilized dimer
Function / homology
Function and homology information


ferredoxin-NAD(P) reductase activity / regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / apicoplast / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / FAD binding / electron transfer activity / identical protein binding
Similarity search - Function
Ferredoxin--NADP reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. ...Ferredoxin--NADP reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / CITRATE ANION / Ferredoxin--NADP reductase, apicoplast / :
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMilani, M. / Mastrangelo, E. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Ferredoxin-NADP(+) Reductase from Plasmodium falciparum Undergoes NADP(+)-dependent Dimerization and Inactivation: Functional and Crystallographic Analysis.
Authors: Milani, M. / Balconi, E. / Aliverti, A. / Mastrangelo, E. / Seeber, F. / Bolognesi, M. / Zanetti, G.
History
DepositionJan 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 6, 2014Group: Structure summary
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 / 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: Putative ferredoxin--NADP reductase
B: Putative ferredoxin--NADP reductase
C: Putative ferredoxin--NADP reductase
D: Putative ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,78410
Polymers149,2644
Non-polymers3,5206
Water5,242291
1
A: Putative ferredoxin--NADP reductase
B: Putative ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5816
Polymers74,6322
Non-polymers1,9494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-27 kcal/mol
Surface area24390 Å2
MethodPISA
2
C: Putative ferredoxin--NADP reductase
D: Putative ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2034
Polymers74,6322
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-26 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.038, 138.038, 147.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Putative ferredoxin--NADP reductase / E.C.1.18.1.2 / Ferredoxin--nadp reductase / putative


Mass: 37315.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Species: Plasmodium falciparum / Strain: isolate 3D7 / Gene: ORF PFF1115w / Production host: Escherichia coli (E. coli)
References: UniProt: Q6LF82, UniProt: C6KT68*PLUS, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.4
Details: NH4 Acetate 0.2 M, PEG 4000 22 % , pH 5.4, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→90 Å / Num. all: 63426 / Num. obs: 63426 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.9 / Num. unique all: 9180 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24569 3191 5 %RANDOM
Rwork0.19544 ---
all0.19794 60440 --
obs0.19794 60066 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.896 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å20 Å2
2---0.29 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8720 0 238 291 9249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.97712474
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37951027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05724.442466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94151564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9451526
X-RAY DIFFRACTIONr_chiral_restr0.0880.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026950
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.24012
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26165
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.06725187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.68938418
X-RAY DIFFRACTIONr_scbond_it4.59444021
X-RAY DIFFRACTIONr_scangle_it6.71464056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 221 -
Rwork0.259 4381 -
obs--99.68 %

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