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- PDB-1ogj: FERREDOXIN:NADP+ REDUCTASE MUTANT WITH LEU 263 REPLACED BY PRO (L263P) -

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Basic information

Entry
Database: PDB / ID: 1ogj
TitleFERREDOXIN:NADP+ REDUCTASE MUTANT WITH LEU 263 REPLACED BY PRO (L263P)
ComponentsFERREDOXIN--NADP+ REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / NADP / FAD / FNR / NADP REDUCTASE
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / 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 / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.64 Å
AuthorsHermoso, J.A. / Mayoral, T. / Martinez Julvez, M. / Medina, M. / Sanz-Aparicio, J. / Gomez-Moreno, C.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Involvement of the Pyrophosphate and the 2'-Phosphate Binding Regions of Ferredoxin-Nadp+ Reductase in Coenzyme Specificity
Authors: Tejero, J. / Martinez-Julvez, M. / Mayoral, T. / Luquita, A. / Sanz-Aparicio, J. / Hermoso, J.A. / Hurley, J. / Tollin, G. / Gomez-Moreno, C. / Medina, M.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: X-Ray Structure of the Ferredoxin:Nadp+ Reductase from the Cyanobacterium Anabanena Pcc 7119 at 1.8A Resolution, and Crystallographic Studies of Nadp Binding at 2.25A Resolution
Authors: Serre, L. / Vellieux, F.M.D. / Medina, M. / Gomez-Moreno, C. / Fontecilla, J.C. / Frey, M.
History
DepositionMay 6, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2003Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 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 / 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

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Assembly

Deposited unit
A: FERREDOXIN--NADP+ REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9073
Polymers34,0261
Non-polymers8822
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.260, 87.260, 96.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein FERREDOXIN--NADP+ REDUCTASE


Mass: 34025.633 Da / Num. of mol.: 1 / Fragment: RESDIUES 138-440 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (STRAIN PCC 7119) (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION LEU400PRO THE PROTEIN IS FROM CYANOBACTERIUM ANABAENA.

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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: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-HCl1droppH8.0
25 %(w/v)beta-octylglucoside1drop
318-20 %(w/v)PEG60001reservoir
420 mMammonium sulfate1reservoir
50.1 MMES-NaOH1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.637→20.498 Å / Num. obs: 51351 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 13.1 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 0.053
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 0.281 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 1.63 Å / Lowest resolution: 20.49 Å / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Highest resolution: 1.63 Å / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1QUE

1que


Resolution: 1.64→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1491595.24 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3621 7.1 %RANDOM
Rwork0.207 ---
obs0.207 51304 99.6 %-
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å21.19 Å20 Å2
2--1.81 Å20 Å2
3----3.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.64→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 58 355 2750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 394 7.2 %
Rwork0.31 5063 -
obs--59.6 %
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 19.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.23

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