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- PDB-5ygq: Crystal Structure of Ferredoxin NADP+ Oxidoreductase from Rhodops... -

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Basic information

Entry
Database: PDB / ID: 5ygq
TitleCrystal Structure of Ferredoxin NADP+ Oxidoreductase from Rhodopseudomonas palustris
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / electron transport / fad / flavoprotein / nadp
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Ferredoxin--NADP reductase, type 2 / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMuraki, N. / Seo, D. / Kurisu, G.
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2019
Title: Kinetic and structural insight into a role of the re-face Tyr328 residue of the homodimer type ferredoxin-NADP+oxidoreductase from Rhodopseudomonas palustris in the reaction with NADP+/NADPH.
Authors: Seo, D. / Muraki, N. / Kurisu, G.
History
DepositionSep 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase
B: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6824
Polymers74,1112
Non-polymers1,5712
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-43 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.868, 81.227, 122.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 3 - 341 / Label seq-ID: 3 - 341

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ferredoxin--NADP reductase / Fd-NADP(+) reductase


Mass: 37055.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA3954 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N2U4, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium iodide, Tris-HCl pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27560 / % possible obs: 98.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.3 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ab1

3ab1


Resolution: 2.4→36.42 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.893 / SU B: 23.465 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.645 / ESU R Free: 0.302 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26324 1341 5 %RANDOM
Rwork0.21829 ---
obs0.22053 25218 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å20 Å2
2--0.28 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.4→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 106 51 5336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195419
X-RAY DIFFRACTIONr_bond_other_d0.0080.025238
X-RAY DIFFRACTIONr_angle_refined_deg2.1432.0027375
X-RAY DIFFRACTIONr_angle_other_deg1.604312094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3955683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81325.283212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65115905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6371518
X-RAY DIFFRACTIONr_chiral_restr0.1290.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216047
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021133
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8284.1532732
X-RAY DIFFRACTIONr_mcbond_other2.8284.1522731
X-RAY DIFFRACTIONr_mcangle_it4.5516.2183415
X-RAY DIFFRACTIONr_mcangle_other4.5516.2193416
X-RAY DIFFRACTIONr_scbond_it2.5414.3712687
X-RAY DIFFRACTIONr_scbond_other2.5414.3712688
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1366.4243961
X-RAY DIFFRACTIONr_long_range_B_refined6.64431.835923
X-RAY DIFFRACTIONr_long_range_B_other6.64131.8315919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 37210 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.404→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 85 -
Rwork0.279 1287 -
obs--67.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2682-0.32160.00380.4845-0.0170.0037-0.0323-0.020.02670.07550.029-0.0242-0.0202-0.00040.00340.15720.0060.00340.0030.00510.039215.73211.65329.4771
20.05230.0788-0.11350.8578-0.06630.2652-0.0022-0.01040.0037-0.12980.0249-0.0386-0.00030.0271-0.02270.1719-0.0075-0.00760.0048-0.00040.020210.7848.13423.7589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 342
2X-RAY DIFFRACTION2allB3 - 342

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