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- PDB-3mhp: FNR-recruitment to the thylakoid -

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Basic information

Entry
Database: PDB / ID: 3mhp
TitleFNR-recruitment to the thylakoid
Components
  • Ferredoxin--NADP reductase, leaf isozyme, chloroplastic
  • TIC62_peptide
KeywordsOXIDOREDUCTASE / FNR / thylakoid membrane / proton-flux / poly proline II helix / self assembly / NADP(H)
Function / homology
Function and homology information


chloroplast thylakoid membrane protein complex / chloroplast inner membrane / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / chloroplast stroma / photosynthesis / electron transport chain / protein transport
Similarity search - Function
NAD(P)H-binding / Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / NAD(P)-binding 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 ...NAD(P)H-binding / Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / NAD(P)-binding 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 / NAD(P)-binding domain superfamily / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase, leaf isozyme, chloroplastic / Protein TIC 62, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGroll, M. / Alte, F. / Soll, J. / Boelter, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Ferredoxin:NADPH oxidoreductase is recruited to thylakoids by binding to a polyproline type II helix in a pH-dependent manner.
Authors: Alte, F. / Stengel, A. / Benz, J.P. / Petersen, E. / Soll, J. / Groll, M. / Bolter, B.
History
DepositionApr 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase, leaf isozyme, chloroplastic
B: Ferredoxin--NADP reductase, leaf isozyme, chloroplastic
C: TIC62_peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5485
Polymers69,9773
Non-polymers1,5712
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-35 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.463, 48.824, 71.349
Angle α, β, γ (deg.)106.56, 97.01, 91.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ferredoxin--NADP reductase, leaf isozyme, chloroplastic / FNR


Mass: 33564.609 Da / Num. of mol.: 2 / Fragment: UNP residues 66-360, FAD-binding FR-type domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: PETH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P10933, ferredoxin-NADP+ reductase
#2: Protein/peptide TIC62_peptide


Mass: 2848.139 Da / Num. of mol.: 1 / Fragment: UNP residues 383-408 / Source method: obtained synthetically
Details: The TIC62 sequence occurs naturally in Pisum sativum. The 27mer has been synthesized by solid-phase peptide synthesis
References: UniProt: Q8SKU2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200 mM Ammoniumcitrate 20 % PEG 3350 crystal growth - 3 month, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 1, 2009 / Details: Mirrows
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→60 Å / Num. all: 66969 / Num. obs: 66902 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 23.6
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.236 / Num. unique all: 10509 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
CNS1.2refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QG0

1qg0


Resolution: 1.7→14.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 59157.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3386 5.1 %RANDOM
Rwork0.181 ---
obs0.181 66707 99.7 %-
all-66802 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.4188 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.42 Å21.28 Å2
2--0.28 Å2-0.05 Å2
3---0.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 106 513 5480
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.962.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.7→1.8 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 552 5 %
Rwork0.209 10546 -
obs-10509 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4fad.par

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