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- PDB-3lvb: Crystal structure of the Ferredoxin:NADP+ reductase from maize ro... -

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Basic information

Entry
Database: PDB / ID: 3lvb
TitleCrystal structure of the Ferredoxin:NADP+ reductase from maize root at 1.7 angstroms - Test Set Withheld
ComponentsFerredoxin-NADP reductase
KeywordsOXIDOREDUCTASE / electron transport
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / NADPH binding / photosynthesis / electron transport chain / electron transfer activity
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
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFaber, H.R. / Karplus, P.A. / Aliverti, A. / Ferioli, C. / Spinola, M.
Citation
Journal: Biochemistry / Year: 2001
Title: Biochemical and crystallographic characterization of ferredoxin-NADP(+) reductase from nonphotosynthetic tissues
Authors: Aliverti, A. / Faber, R. / Finnerty, C.M. / Ferioli, C. / Pandini, V. / Negri, A. / Karplus, P.A. / Zanetti, G.
#1: Journal: To be Published
Title: Using a conformationally dependent stereochemical library improves refinement
Authors: Tronrud, D.E. / Berkholz, D.S. / Karplus, P.A.
History
DepositionFeb 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 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_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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)35,6342
Polymers34,8481
Non-polymers7861
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.670, 59.670, 189.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is the contents of the asymmetric unit

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Components

#1: Protein Ferredoxin-NADP reductase


Mass: 34848.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: Q41736, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, Na cacodylate, Mg Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2000 / Details: Yale Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 47556 / Num. obs: 47556 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3 / % possible all: 96.1

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Processing

Software
NameClassification
mrxmodel building
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
mrxphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FNB

1fnb


Resolution: 1.7→23.94 Å / Isotropic thermal model: isotropic / Cross valid method: throughhout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 4370 -random
Rwork0.164 ---
all0.17 43687 --
obs0.17 43687 99 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.14 Å21.14 Å20 Å2
2--1.14 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 53 274 2779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.027
X-RAY DIFFRACTIONt_dihedral_angle_d17.04
X-RAY DIFFRACTIONt_plane_rms0.018
X-RAY DIFFRACTIONt_trig_c_planes0.017
X-RAY DIFFRACTIONt_chiral_count0
X-RAY DIFFRACTIONt_bcorrel4.49

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