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- PDB-3jqq: Crystal structure of the H286K mutant of Ferredoxin-NADP+ reducta... -

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Basic information

Entry
Database: PDB / ID: 3jqq
TitleCrystal structure of the H286K mutant of Ferredoxin-NADP+ reductase from Plasmodium falciparum in complex with 2'P-AMP
ComponentsFerredoxin NADP reductase
KeywordsOXIDOREDUCTASE / Ferredoxin-NADP+ reductase / FAD
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 (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCanevari, G. / Milani, M. / Bolognesi, M.
CitationJournal: Biochemistry / Year: 2009
Title: Plasmodium falciparum ferredoxin-NADP+ reductase His286 plays a dual role in NADP(H) binding and catalysis
Authors: Crobu, D. / Canevari, G. / Milani, M. / Pandini, V. / Vanoni, M.A. / Bolognesi, M. / Zanetti, G. / Aliverti, A.
History
DepositionSep 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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: Ferredoxin NADP reductase
B: Ferredoxin NADP reductase
C: Ferredoxin NADP reductase
D: Ferredoxin NADP reductase
E: Ferredoxin NADP reductase
F: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,11918
Polymers223,8426
Non-polymers7,27712
Water20,8971160
1
A: Ferredoxin NADP reductase
B: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0406
Polymers74,6142
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-23.7 kcal/mol
Surface area24410 Å2
MethodPISA
2
C: Ferredoxin NADP reductase
D: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0406
Polymers74,6142
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-24.2 kcal/mol
Surface area24200 Å2
MethodPISA
3
E: Ferredoxin NADP reductase
F: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0406
Polymers74,6142
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-31.4 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.243, 124.243, 134.255
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
Ferredoxin NADP reductase


Mass: 37307.023 Da / Num. of mol.: 6 / Fragment: residues in UNP 56-371 / Mutation: H286K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PfFNR, PFF1115w / Plasmid: pET-PfFNR-H286K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: C6KT68, ferredoxin-NADP+ reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


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


Mass: 18.015 Da / Num. of mol.: 1160 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 293 K / Method: microbatch with permeable oil / pH: 5.4
Details: 20% isopropanol, 20% PEG 4000, 0.1M citrate-NaOH, 2mM 2'P-AMP(Cocrystallization), pH 5.4, Microbatch with permeable oil, 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: Aug 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→83.918 Å / Num. all: 117739 / Num. obs: 117739 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 1.8 / Num. unique all: 17208 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OK7

2ok7


Resolution: 2.2→62.12 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.303 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30797 5894 5 %RANDOM
Rwork0.2562 ---
all0.25879 111762 --
obs0.25879 111762 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.724 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20.94 Å20 Å2
2--1.88 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.2→62.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13096 0 480 1160 14736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.99318890
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09451533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64124.459693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32152368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1461542
X-RAY DIFFRACTIONr_chiral_restr0.070.21977
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210410
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1281.57767
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.677212593
X-RAY DIFFRACTIONr_scbond_it0.51636163
X-RAY DIFFRACTIONr_scangle_it0.8814.56297
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 439 -
Rwork0.308 8334 -
obs--99.95 %

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