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

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Basic information

Entry
Database: PDB / ID: 2vnk
TitleX-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH NADP. FORM III AT 1.93 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
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavodoxin/ferredoxin--NADP reductase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: NADPH\:FERREDOXIN REDUCTASE
B: NADPH\:FERREDOXIN REDUCTASE
C: NADPH\:FERREDOXIN REDUCTASE
D: NADPH\:FERREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,86312
Polymers121,7484
Non-polymers6,1168
Water15,889882
1
A: NADPH\:FERREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9663
Polymers30,4371
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NADPH\:FERREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9663
Polymers30,4371
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: NADPH\:FERREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9663
Polymers30,4371
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: NADPH\:FERREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9663
Polymers30,4371
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.382, 93.446, 104.936
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, -0.0025, 0.0021), (-0.0025, 1, -0.0024), (-0.0021, -0.0024, -1)34.7007, 0.0947, 57.5357
2given(1, -0.0007), (-1, 0.0007), (-0.0007, -0.0007, -1)0.0352, 34.8117, 52.5018
3given(-1, 0.0026, -0.0014), (-0.0026, -1, 0.0019), (-0.0014, 0.0019, 1)34.7051, 34.8118, 4.9828

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Components

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


Mass: 30436.889 Da / Num. of mol.: 4
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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.83 Å3/Da / Density % sol: 56.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.93→49.21 Å / Num. obs: 122712 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 1.93→2.12 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.2 / % possible all: 89

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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: 1.93→49.21 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
Details: THE FIRST 15 RESIDUES OF THE POLYPEPTIDE CHAIN AND THE NMN MOIETY OF THE NADP ARE NOT INCLUDED IN THE CHAINS A, B, C AND D OF THE MODEL DUE TO THEY ARE NOT OBSERVED IN THE ELECTRON DENSITY ...Details: THE FIRST 15 RESIDUES OF THE POLYPEPTIDE CHAIN AND THE NMN MOIETY OF THE NADP ARE NOT INCLUDED IN THE CHAINS A, B, C AND D OF THE MODEL DUE TO THEY ARE NOT OBSERVED IN THE ELECTRON DENSITY MAP. RESIDUES 270-272 OF CHAINS B AND D ARE NOT INCLUDED IN THE MODEL DUE TO POOR QUALITY OF THE ELECTRON DENSITY MAP IN THESE POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22615 4766 5 %RANDOM
Rwork0.20008 ---
obs0.20008 90099 94.3 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.772 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20.02 Å2
2---0.15 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.93→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8080 0 336 882 9298
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.791.5
X-RAY DIFFRACTIONc_mcangle_it1.52
X-RAY DIFFRACTIONc_scbond_it2.123
X-RAY DIFFRACTIONc_scangle_it3.64.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 290
Rwork0.249 5751

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