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- PDB-2bgj: X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobac... -

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Basic information

Entry
Database: PDB / ID: 2bgj
TitleX-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus at 2.1 Angstroms
ComponentsFERREDOXIN-NADP(H) REDUCTASE
KeywordsOXIDOREDUCTASE / FERREDOXIN(FLAVODOXIN)-NADP(H) REDUCTASE / FLAVOPROTEINS / ELECTRON TRANSFER / RHODOBACTER CAPSULATUS
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 / Flavodoxin/ferredoxin--NADP reductase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPerez-Dorado, J.I. / Hermoso, J.A. / Nogues, I. / Frago, S. / Bittel, C. / Mayhew, S.G. / Gomez-Moreno, C. / Medina, M. / Cortez, N. / Carrillo, N.
Citation
Journal: Biochemistry / Year: 2005
Title: The ferredoxin-NADP(H) reductase from Rhodobacter capsulatus: molecular structure and catalytic mechanism.
Authors: Nogues, I. / Perez-Dorado, I. / Frago, S. / Bittel, C. / Mayhew, S.G. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M. / Cortez, N. / Carrillo, N.
#1: 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, J.I. / Bittel, C. / Cortez, N. / Hermoso, J.A.
#2: 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
DepositionDec 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN-NADP(H) REDUCTASE
B: FERREDOXIN-NADP(H) REDUCTASE
C: FERREDOXIN-NADP(H) REDUCTASE
D: FERREDOXIN-NADP(H) REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8908
Polymers121,7484
Non-polymers3,1424
Water6,323351
1
A: FERREDOXIN-NADP(H) REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2222
Polymers30,4371
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN-NADP(H) REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2222
Polymers30,4371
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FERREDOXIN-NADP(H) REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2222
Polymers30,4371
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FERREDOXIN-NADP(H) REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2222
Polymers30,4371
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.290, 93.626, 103.427
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 3.0E-5, -1.0E-5), (3.0E-5, 1, -2.0E-5), (1.0E-5, -2.0E-5, -1)34.53708, -0.02099, 56.93575
2given(0.99996, 0.00685, -0.00484), (0.00686, -0.99997, 0.00192), (-0.00483, -0.00195, -0.99999)0.36732, 35.11992, 51.93135
3given(-0.99996, -0.00688, 0.00483), (0.00689, -0.99997, 0.00194), (0.00482, 0.00197, 0.99999)34.19625, 35.11736, -5.4441

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Components

#1: Protein
FERREDOXIN-NADP(H) REDUCTASE


Mass: 30436.889 Da / Num. of mol.: 4 / Mutation: YES
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.8 Å3/Da / Density % sol: 56 %
Description: STARTING MODEL USED FOR THE MOLECULAR REPLACEMENT WAS THE REFINED FPR MODEL OBTAINED IN PRESENCE OF THE DETERGENT N- HEPTYL-BETA-DTHIOGLUCOSIDE
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2004 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→22.8 Å / Num. obs: 73447 / % possible obs: 80.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / % possible all: 60.4

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→105.41 Å / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24322 3071 5 %RANDOM
Rwork0.21555 ---
obs0.21555 57974 79.14 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.148 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-0.23 Å2
2---0.24 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.1→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 212 351 8711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.353
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d5.28
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_it0.9451.5
X-RAY DIFFRACTIONc_mcangle_it1.7672
X-RAY DIFFRACTIONc_scbond_it2.1883
X-RAY DIFFRACTIONc_scangle_it3.6564.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 0.84 Å2 / Rms dev position: 0.46 Å / Weight Biso : 2 / Weight position: 0.5
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 183
Rwork0.303 3069

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