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- PDB-3jqp: Crystal structure of the H286L mutant of Ferredoxin-NADP+ reducta... -

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Basic information

Entry
Database: PDB / ID: 3jqp
TitleCrystal structure of the H286L mutant of Ferredoxin-NADP+ reductase from Plasmodium falciparum with 2'P-AMP
ComponentsFerredoxin NADP reductase
KeywordsOXIDOREDUCTASE / Ferredoxin-NADP+ reductase from Plasmodium falciparum / FAD
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 / 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: 3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)231,02318
Polymers223,7466
Non-polymers7,27712
Water2,990166
1
A: Ferredoxin NADP reductase
B: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0086
Polymers74,5822
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ferredoxin NADP reductase
D: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0086
Polymers74,5822
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ferredoxin NADP reductase
F: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0086
Polymers74,5822
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Ferredoxin NADP reductase
hetero molecules

B: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0086
Polymers74,5822
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x+y-1,-x-1,z-1/31
Buried area6770 Å2
ΔGint-27 kcal/mol
Surface area24520 Å2
MethodPISA
5
C: Ferredoxin NADP reductase
hetero molecules

D: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0086
Polymers74,5822
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+1/31
Buried area6670 Å2
ΔGint-28 kcal/mol
Surface area24790 Å2
MethodPISA
6
E: Ferredoxin NADP reductase
hetero molecules

F: Ferredoxin NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0086
Polymers74,5822
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x+y-1,-x,z-1/31
Buried area6750 Å2
ΔGint-31 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.570, 122.570, 133.744
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: 37291.000 Da / Num. of mol.: 6 / Fragment: residues in UNP 56-371 / Mutation: H286L
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-H286L / 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.: 166 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293 K / Method: microbatch, permeable oil / pH: 6.5
Details: 12% PEG 6000, 5% glycerol, 0.1 M cacodylate-NaOH , pH 6.5, Microbatch, permeable oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 7, 2008
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→56.58 Å / Num. all: 44994 / Num. obs: 44994 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 9.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6554 / % possible all: 99.9

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Processing

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

2ok7


Resolution: 3→56.58 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.824 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31661 2268 5 %RANDOM
Rwork0.24415 ---
all0.24776 42693 --
obs0.24776 42693 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.833 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å21.15 Å20 Å2
2--2.3 Å20 Å2
3----3.45 Å2
Refinement stepCycle: LAST / Resolution: 3→56.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13228 0 480 166 13874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02214060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.99219065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57551551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11824.522701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.982152388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8651541
X-RAY DIFFRACTIONr_chiral_restr0.0850.22013
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110533
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_it1.06122937
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91434766
X-RAY DIFFRACTIONr_scbond_it1.64542290
X-RAY DIFFRACTIONr_scangle_it2.77362322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 191 -
Rwork0.335 3147 -
obs-24091 99.88 %

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