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- PDB-2ok7: Ferredoxin-NADP+ reductase from Plasmodium falciparum with 2'P-AMP -

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Basic information

Entry
Database: PDB / ID: 2ok7
TitleFerredoxin-NADP+ reductase from Plasmodium falciparum with 2'P-AMP
ComponentsPutative ferredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / disulfide-stabilized dimer
Function / homology
Function and homology information


ferredoxin-[NAD(P)H] reductase activity / regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / apicoplast / ferredoxin-NADP+ reductase / 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
ADENOSINE-2'-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase, apicoplast / :
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: Putative ferredoxin--NADP reductase
F: Putative ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,19519
Polymers223,8966
Non-polymers7,29913
Water4,107228
1
A: Putative ferredoxin--NADP reductase
B: Putative ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0807
Polymers74,6322
Non-polymers2,4485
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-44 kcal/mol
Surface area24590 Å2
MethodPISA
2
C: Putative ferredoxin--NADP reductase
D: Putative ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0576
Polymers74,6322
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-29 kcal/mol
Surface area25050 Å2
MethodPISA
3
E: Putative ferredoxin--NADP reductase
F: Putative ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0576
Polymers74,6322
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-29 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.129, 123.129, 133.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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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.: 6
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: PEG 4000 25%, buffer Na cacodylate, Na acetate 0.2 M, pH 6., microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.7→60 Å / Num. all: 61398 / Num. obs: 61398 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8933 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jb9

1jb9


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.817 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.392 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32083 3082 5 %RANDOM
Rwork0.25998 ---
all0.26303 59148 --
obs0.26303 58273 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.137 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å20 Å2
2--1.44 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12949 0 481 228 13658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02213794
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.98818729
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93351532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17724.446677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.435152279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8431535
X-RAY DIFFRACTIONr_chiral_restr0.0870.21967
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210323
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.130.35657
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.58977
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.5791
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0880.387
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.522
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.01327748
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.893312526
X-RAY DIFFRACTIONr_scbond_it10.23146046
X-RAY DIFFRACTIONr_scangle_it11.76966203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 227 -
Rwork0.337 4266 -
obs--98.16 %

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