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- PDB-6rra: X-RAY STRUCTURE OF THE FERREDOXIN-NADP REDUCTASE FROM BRUCELLA OV... -

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Basic information

Entry
Database: PDB / ID: 6rra
TitleX-RAY STRUCTURE OF THE FERREDOXIN-NADP REDUCTASE FROM BRUCELLA OVIS IN COMPLEX WITH NADP
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / heme catabolic process / cellular response to oxidative stress / nucleotide binding
Similarity search - Function
: / Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-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 ...: / Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-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 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMartinez-Julvez, M. / Taleb, V. / Medina, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-75183-P Spain
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2019
Title: Towards the competent conformation for catalysis in the ferredoxin-NADP+reductase from the Brucella ovis pathogen.
Authors: Perez-Amigot, D. / Taleb, V. / Boneta, S. / Anoz-Carbonell, E. / Sebastian, M. / Velazquez-Campoy, A. / Polo, V. / Martinez-Julvez, M. / Medina, M.
History
DepositionMay 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,9944
Polymers29,3691
Non-polymers1,6253
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-19 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.639, 70.753, 84.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ferredoxin--NADP reductase


Mass: 29369.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) (bacteria)
Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: fpr, BOV_0348 / Variant: ATCC 25840 / 63/290 / NCTC 10512 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3ASL8, 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Soaking of crystals generated in 2% PEG 400, 0.1 M HEPES pH 7.5 and 2 M ammonium sulphate, with a 10 mM of NADP+ solution for 25 min.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.4→84.24 Å / Num. obs: 69102 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9824 / CC1/2: 0.811 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QDX

2qdx


Resolution: 1.4→54.18 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.202 -4.9 %
Rwork0.17985 --
obs0.18096 65678 99.1 %
Refinement stepCycle: LAST / Resolution: 1.4→54.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 106 257 2433

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