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- PDB-2vzl: FERREDOXIN-NADP REDUCTASE (MUTATIONS: T155G, A160T, L263P AND Y30... -

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Basic information

Entry
Database: PDB / ID: 2vzl
TitleFERREDOXIN-NADP REDUCTASE (MUTATIONS: T155G, A160T, L263P AND Y303S) COMPLEXED WITH NAD BY COCRYSTALLIZATION
ComponentsFERREDOXIN-NADP REDUCTASE
KeywordsOXIDOREDUCTASE / PHYCOBILISOME / FAD / NADP / MEMBRANE / THYLAKOID / FLAVOPROTEIN
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesNOSTOC SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsHerguedas, B. / Martinez-Julvez, M. / Hermoso, J.A. / Peregrina, J.R. / Medina, M.
CitationJournal: Biochemistry / Year: 2009
Title: Protein Motifs Involved in Coenzyme Interaction and Enzymatic Efficiency in Anabaena Ferredoxin-Nadp+ Reductase.
Authors: Peregrina, J.R. / Herguedas, B. / Hermoso, J.A. / Martinez-Julvez, M. / Medina, M.
History
DepositionJul 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 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: FERREDOXIN-NADP REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6094
Polymers34,0681
Non-polymers1,5413
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.888, 86.888, 96.372
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein FERREDOXIN-NADP REDUCTASE


Mass: 34067.691 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-440 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NOSTOC SP. (bacteria) / Strain: PCC 7119 / Plasmid: PET 28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 / References: UniProt: P21890, 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 292 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 297 TO THR ...ENGINEERED RESIDUE IN CHAIN A, THR 292 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 297 TO THR ENGINEERED RESIDUE IN CHAIN A, LEU 400 TO PRO ENGINEERED RESIDUE IN CHAIN A, TYR 440 TO SER
Nonpolymer detailsNICOTINAMIDE-ADENINE-DINUCLEOTIDE (NAD): ONLY ADP MOEITY IS OBSERVED TWO ALTERNATE CONFORMATIONS ...NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NAD): ONLY ADP MOEITY IS OBSERVED TWO ALTERNATE CONFORMATIONS FOR PYROPHOSPHATE-A AND B-ARE OBSERVED-OCCUPANCY 0.5 FOR EACH ATOM.
Sequence detailsFNR MUTANT (T155G, A160T, L263P, Y303S)

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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: 2.92 Å3/Da / Density % sol: 57.8 % / Description: NONE
Crystal growpH: 5.5
Details: 20% PEG 6000 0.1M ACNA, PH 5.5 B-OCTYL GLYCOSIDE AT 2%(W/V) 10-60 MM NAD

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER-NONIUS / Wavelength: 1.5418
DetectorType: BRUKER-NONIUS / Detector: CCD / Date: Dec 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→43.44 Å / Num. obs: 31094 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4
Reflection shellResolution: 1.93→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.47 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QUE

1que


Resolution: 1.93→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.605 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2185 7 %RANDOM
Rwork0.169 ---
obs0.17 28836 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 86 429 2845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212486
X-RAY DIFFRACTIONr_bond_other_d0.0020.022173
X-RAY DIFFRACTIONr_angle_refined_deg1.0492.0063386
X-RAY DIFFRACTIONr_angle_other_deg0.71435098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1265294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02457
X-RAY DIFFRACTIONr_nbd_refined0.1770.2458
X-RAY DIFFRACTIONr_nbd_other0.2310.22556
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0760.21335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0610.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5311.51466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00522371
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.22631020
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1584.51015
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 169
Rwork0.232 2081

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