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- PDB-2vni: X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBAC... -

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Basic information

Entry
Database: PDB / ID: 2vni
TitleX-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH 2P-AMP AT 2.37 ANGSTROMS RESOLUTION
ComponentsNADPH\:FERREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER / RHODOBACTER CAPSULATUS / FERREDOXIN(FLAVODOXIN)-NADP(H) REDUCTASE / NADP / FLAVOPROTEINS
Function / homology
Function and homology information


flavodoxin-NADP+ reductase / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / heme catabolic process / cellular response to oxidative stress / nucleotide binding / cytoplasm
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
ADENOSINE-2'-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Flavodoxin/ferredoxin--NADP reductase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsPerez-Dorado, I. / Hermoso, J.A.
Citation
Journal: Biochim.Biophys.Acta / Year: 2009
Title: Coenzyme Binding and Hydride Transfer in Rhodobacter Capsulatus Ferredoxin/Flavodoxin Nadp(H) Oxidoreductase.
Authors: Bortolotti, A. / Perez-Dorado, I. / Goni, G. / Medina, M. / Hermoso, J.A. / Carrillo, N. / Cortez, N.
#1: Journal: Biochemistry / Year: 2005
Title: The Feredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus: Molecular Structure and Catalytic Mechanism
Authors: Nogues, I. / Perez-Dorado, I. / Frago, S. / Bittel, C. / Mayhew, S. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M. / Cortez, N. / Carrillo, N.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Ferredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus
Authors: Perez-Dorado, I. / Bittel, C. / Cortez, N. / Hermoso, J.A.
#3: Journal: FEBS Lett. / Year: 2003
Title: The Oxidant-Responsive Diaphorase of Rhodobacter Capsulatus is a Ferredoxin (Flavodoxin)-Nadp(H) Reductase
Authors: Bittel, C. / Tabares, L.C. / Armesto, M. / Carrillo, N. / Cortez, N.
History
DepositionFeb 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: NADPH\:FERREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9444
Polymers30,4371
Non-polymers1,5073
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)121.116, 121.116, 50.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein NADPH\:FERREDOXIN REDUCTASE / FERREDOXIN-NADP REDUCTASE


Mass: 30436.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Strain: 37B4 / Variant: DSM938 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9L6V3, 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-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Sugar ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.57 Å3/Da / Density % sol: 65.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorDate: Jun 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.24→45.56 Å / Num. obs: 24368 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 2.24→2.73 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.8 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BGI

2bgi


Resolution: 2.24→45.56 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1746057.61 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FIRST 15 RESIDUES ARE NOT INCLUDED IN THE MODEL DUE TO THEY ARE NOT OBSERVED IN THE ELECTRON DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.267 982 4.8 %RANDOM
Rwork0.229 ---
obs0.229 20422 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4491 Å2 / ksol: 0.350607 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.03 Å27.27 Å20 Å2
2--8.03 Å20 Å2
3----16.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.24→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 99 73 2203
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.24→2.38 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 153 4.7 %
Rwork0.309 3110 -
obs--94.9 %

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