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- PDB-1que: X-RAY STRUCTURE OF THE FERREDOXIN:NADP+ REDUCTASE FROM THE CYANOB... -

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Basic information

Entry
Database: PDB / ID: 1que
TitleX-RAY STRUCTURE OF THE FERREDOXIN:NADP+ REDUCTASE FROM THE CYANOBACTERIUM ANABAENA PCC 7119 AT 1.8 ANGSTROMS
ComponentsFERREDOXIN--NADP+ REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / NADP / FAD / THYLAKOID MEMBRANE / HYCOBILISOME / FNR / NADP+ REDUCTASE
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 / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsSerre, L. / Frey, M. / Vellieux, F.M.D.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: X-ray structure of the ferredoxin:NADP+ reductase from the cyanobacterium Anabaena PCC 7119 at 1.8 A resolution, and crystallographic studies of NADP+ binding at 2.25 A resolution.
Authors: Serre, L. / Vellieux, F.M. / Medina, M. / Gomez-Moreno, C. / Fontecilla-Camps, J.C. / Frey, M.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystals of Anabaena Pcc 7119 Ferredoxin-Nadp+ Reductase
Authors: Serre, L. / Medina, M. / Gomez-Moreno, C. / Fontecilla-Camps, J.C. / Frey, M.
#2: Journal: Nucleic Acids Res. / Year: 1990
Title: Sequence of the Ferredoxin-Nadp(+)-Reductase Gene from Anabaena Pcc 7119
Authors: Fillat, M.F. / Bakker, H.A. / Weisbeek, P.J.
History
DepositionJul 6, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / refine
Item: _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model

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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)34,9233
Polymers34,0421
Non-polymers8822
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.200, 88.200, 97.100
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 / FNR


Mass: 34041.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / Strain: PCC 7119 / References: UniProt: P21890, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: SEE REFERENCE 1., pH 7.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.6 mg/mlprotein1drop
24 mMTris-HCl1drop
31 %(w/v)beta-OG1drop
48 %(w/v)PEG60001drop
58 mMammonium sulfate1drop
60.04 %(w/v)sodium azide1drop
70.04 MMES-NaOH1drop
820 %(w/v)PEG60001reservoir
920 mMammonium sulfate1reservoir
100.1 %(w/v)sodium azide1reservoir
110.1 MMES-NaOH1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1992
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 20337 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.07
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3 % / % possible all: 34
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 96286 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 34 %

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Processing

Software
NameVersionClassification
PHASEmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
BIOMOL(KBRANI)data scaling
PHASESphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→15 Å / Cross valid method: FREE-R / σ(F): 4
Details: THE INITIAL MODEL WAS BUILT IN A M.I.R SOLVENT FLATTENED ELECTRON DENSITY MAP AT 2.6 ANGSTROMS RESOLUTION WITH THE SPINACH FNR MODEL AS A GUIDE (KARPLUS, DANIELS, HERRIOTT, SCIENCE 1991, 251 ...Details: THE INITIAL MODEL WAS BUILT IN A M.I.R SOLVENT FLATTENED ELECTRON DENSITY MAP AT 2.6 ANGSTROMS RESOLUTION WITH THE SPINACH FNR MODEL AS A GUIDE (KARPLUS, DANIELS, HERRIOTT, SCIENCE 1991, 251 60-66). RESIDUES 1 - 8 AND 106 - 112 ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP AND THEY HAVE BEEN TENTATIVELY MODELED. WATER MOLECULES HAVE BEEN NUMBERED ACCORDING THE INCREASING VALUES OF THEIR TEMPERATURE FACTORS STARTING WITH 401. WATER SITES CLOSER THAN 2.5 ANGSTROMS TO PROTEIN ATOMS OR OTHER WATER SITES REFLECTS, MOST PROBABLY, DISORDER.
RfactorNum. reflection% reflection
Rfree0.214 -10 %
Rwork0.172 --
obs0.172 30255 -
Displacement parametersBiso mean: 14.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 15 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 58 325 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.50.9
X-RAY DIFFRACTIONx_mcangle_it21.54
X-RAY DIFFRACTIONx_scbond_it21.28
X-RAY DIFFRACTIONx_scangle_it22.07
LS refinement shellResolution: 1.8→1.82 Å
RfactorNum. reflection% reflection
Rfree0.246 -10 %
Rwork0.2125 463 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSX.PROTOPHCSX.PRO
X-RAY DIFFRACTION2

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