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- PDB-3vo1: Crystal structure of Zea mays leaf ferredoxin-NADP+ reductase II -

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Basic information

Entry
Database: PDB / ID: 3vo1
TitleCrystal structure of Zea mays leaf ferredoxin-NADP+ reductase II
ComponentsFerredoxin
KeywordsOXIDOREDUCTASE / Rossmann Fold / FAD binding
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / photosynthesis / chloroplast / nucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / 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--NADP reductase, plant and Cyanobacteria type / 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
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMuraki, N. / Hase, T. / Kurisu, G.
CitationJournal: Plant Cell / Year: 2012
Title: N-terminal structure of maize ferredoxin:NADP+ reductase determines recruitment into different thylakoid membrane complexes
Authors: Twachtmann, M. / Altmann, B. / Muraki, N. / Voss, I. / Okutani, S. / Kurisu, G. / Hase, T. / Hanke, G.T.
History
DepositionJan 18, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
A: Ferredoxin
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8094
Polymers71,2382
Non-polymers1,5712
Water4,179232
1
A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4042
Polymers35,6191
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4042
Polymers35,6191
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.432, 72.512, 90.407
Angle α, β, γ (deg.)90.00, 99.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ferredoxin / FERREDOXIN-NADP+ REDUCTASE


Mass: 35618.852 Da / Num. of mol.: 2 / Fragment: UNP residues 56-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: L-FNRII / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SLP5, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 45.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 4000, 0.1M ammonium acetate, 0.1M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 3, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 41513 / % possible obs: 98.6 % / Observed criterion σ(F): 0
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.474 / % possible all: 89.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GAW

1gaw


Resolution: 2→40.44 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2281 2945 RANDOM
Rwork0.1945 --
all-42658 -
obs-41496 -
Refinement stepCycle: LAST / Resolution: 2→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 106 232 5040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.23998
X-RAY DIFFRACTIONc_bond_d0.006057
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_mcbond_it1.305
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection
Rfree0.294 173
Rwork0.259 -
obs-3135

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