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- PDB-3vo2: Crystal structure of Zea mays leaf ferredoxin-NADP+ reductase III -

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Basic information

Entry
Database: PDB / ID: 3vo2
TitleCrystal structure of Zea mays leaf ferredoxin-NADP+ reductase III
ComponentsPutative uncharacterized protein
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: 1.39 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: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3194
Polymers69,7482
Non-polymers1,5712
Water10,971609
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6592
Polymers34,8741
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6592
Polymers34,8741
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.673, 76.673, 108.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Putative uncharacterized protein / FERREDOXIN-NADP+ REDUCTASE


Mass: 34873.926 Da / Num. of mol.: 2 / Fragment: UNP residues 61-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / References: UniProt: B4FUM2, 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.: 609 / 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: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 8000, 0.2M sodium chloride, 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: 1.39→50 Å / Num. obs: 136584 / % possible obs: 99.7 % / Observed criterion σ(F): 0
Reflection shellResolution: 1.39→1.44 Å / Rmerge(I) obs: 0.278 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GAW

1gaw


Resolution: 1.39→26.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.988 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21637 7210 5 %RANDOM
Rwork0.19808 ---
obs0.19901 136581 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.562 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.39→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 106 609 5415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225018
X-RAY DIFFRACTIONr_angle_refined_deg1.2112.0026791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60725.113221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66115928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7431522
X-RAY DIFFRACTIONr_chiral_restr0.080.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213756
X-RAY DIFFRACTIONr_mcbond_it0.6261.52992
X-RAY DIFFRACTIONr_mcangle_it1.17724820
X-RAY DIFFRACTIONr_scbond_it1.69832026
X-RAY DIFFRACTIONr_scangle_it2.7864.51971
LS refinement shellResolution: 1.389→1.425 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 524 -
Rwork0.267 10026 -
obs-10026 98.66 %

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