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- PDB-9gxc: Room temperature structure of FAD-containing ferrodoxin-NADP redu... -

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Basic information

Entry
Database: PDB / ID: 9gxc
TitleRoom temperature structure of FAD-containing ferrodoxin-NADP reductase from Brucella ovis at LCLS
Componentsferredoxin--NADP(+) reductase
KeywordsOXIDOREDUCTASE / ferredoxin-NADP+ reductase / room temperature X-ray diffraction / electron transfer / oxidative damage protection / serial femtosecond crystallography / XFEL / microcrystals.
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 / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesBrucella ovis ATCC 25840 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMartinez-Julvez, M. / Martin-Garcia, J.M. / Medina, M.
Funding support Spain, 5items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)PID2022-136369NB-I00 Spain
Other governmentLMP13_21
Other governmentBiologia Estructural_E35_23R
Comunidad de Madrid2019-T1/BMD-15552 Spain
Agencia Estatal de Investigacion (AEI)CNS2022/135713 Spain
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: New insights into the function and molecular mechanisms of Ferredoxin-NADP + reductase from Brucella ovis.
Authors: Moreno, A. / Quereda-Moraleda, I. / Lozano-Vallhonrat, C. / Bunuel-Escudero, M. / Botha, S. / Kupitz, C. / Lisova, S. / Sierra, R. / Mariani, V. / Schleissner, P. / Gee, L.B. / Dorner, K. / ...Authors: Moreno, A. / Quereda-Moraleda, I. / Lozano-Vallhonrat, C. / Bunuel-Escudero, M. / Botha, S. / Kupitz, C. / Lisova, S. / Sierra, R. / Mariani, V. / Schleissner, P. / Gee, L.B. / Dorner, K. / Schmidt, C. / Han, H. / Kloos, M. / Smyth, P. / Valerio, J. / Schulz, J. / de Wijn, R. / Melo, D.V.M. / Round, A. / Trost, F. / Sobolev, E. / Juncheng, E. / Sikorski, M. / Bean, R. / Martinez-Julvez, M. / Martin-Garcia, J.M. / Medina, M.
History
DepositionSep 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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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)31,4902
Polymers30,7051
Non-polymers7861
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-11 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.600, 39.600, 167.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein ferredoxin--NADP(+) reductase


Mass: 30704.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis ATCC 25840 (bacteria) / Gene: fpr, BOV_0348 / Production host: Escherichia coli (E. coli) / 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291.15 K / Method: batch mode / Details: 25% PEG 4.000 0.1M MES pH 6.5 0.2M MgCl2

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.107 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Apr 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.107 Å / Relative weight: 1
ReflectionResolution: 2.1→35.2 Å / Num. obs: 28492 / % possible obs: 100 % / Redundancy: 413 % / CC1/2: 0.9798 / Net I/σ(I): 5.3
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 0.2 / Num. unique obs: 2878 / CC1/2: 0.2043
Serial crystallography sample deliveryDescription: MESH / Method: injection

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
CrystFEL0.10.2data reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→35.2 Å / Cross valid method: FREE R-VALUE / σ(F): 48.25 / Phase error: 22.93 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1967 628 4.82 %
Rwork0.1779 --
obs0.1858 13025 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 53 23 2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.498
X-RAY DIFFRACTIONf_dihedral_angle_d8.89282
X-RAY DIFFRACTIONf_chiral_restr0.041320
X-RAY DIFFRACTIONf_plane_restr0.005373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.77291730.72833053X-RAY DIFFRACTION95
2.42-2.770.31831330.27743125X-RAY DIFFRACTION96
2.77-3.490.26421560.2063106X-RAY DIFFRACTION95
3.49-35.20.14191660.12893113X-RAY DIFFRACTION95

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