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- PDB-8c16: Crystal structure of asymmetric ferredoxin/flavodoxin NADP+ oxido... -

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Basic information

Entry
Database: PDB / ID: 8c16
TitleCrystal structure of asymmetric ferredoxin/flavodoxin NADP+ oxidoreductase 2 (FNR2) H326V mutant from Bacillus cereus
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / FERREDOXIN/FLAVODOXIN REDUCTASE / ELECTRON TRANSFER / FAD / FLAVOPROTEIN / MUTANT
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / 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 superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsRugtveit, A.K. / Hammerstad, M. / Hersleth, H.-P.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway231669 Norway
Research Council of Norway301584 Norway
CitationJournal: Antioxidants / Year: 2023
Title: Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction.
Authors: Hammerstad, M. / Rugtveit, A.K. / Dahlen, S. / Andersen, H.K. / Hersleth, H.P.
History
DepositionDec 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Refinement description / Category: refine_ls_restr_ncs / struct_ncs_dom_lim
Item: _refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_ncs_dom_lim.beg_auth_asym_id ..._refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)148,5876
Polymers147,0164
Non-polymers1,5712
Water00
1
A: Ferredoxin--NADP reductase
B: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2943
Polymers73,5082
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ferredoxin--NADP reductase
C: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2943
Polymers73,5082
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.855, 105.133, 216.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 6 through 318)
d_2ens_1(chain "B" and resid 6 through 318)
d_3ens_1(chain "C" and resid 6 through 318)
d_4ens_1(chain "D" and resid 6 through 318)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 6 - 318 / Label seq-ID: 6 - 318

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2DB
d_3CC
d_4BD

NCS oper:
IDCodeMatrixVector
1given(0.170723071209, 0.980293310168, -0.0993914432809), (-0.263417061697, -0.0517921375349, -0.963290727712), (-0.949455151423, 0.190637353449, 0.249383870581)-16.7122488572, 29.7779404799, 41.7936062746
2given(-0.484999546145, -0.78621146782, 0.382945124147), (-0.779225930314, 0.189744558249, -0.597330689101), (0.396966484437, -0.588105883735, -0.704662387069)-1.14565123108, 29.5909977203, 60.1742545371
3given(-0.283652450423, -0.344300863472, 0.894985029362), (0.380018559768, -0.897262388258, -0.224735624345), (0.880413074415, 0.276364111329, 0.385351393365)-0.0450642134996, 22.7381554105, 6.22027150669

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Components

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


Mass: 36754.094 Da / Num. of mol.: 4 / Mutation: H326V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_4926 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q816D9, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

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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: 56.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24 mg/mL protein (1:1) 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M sodium l-glutamate, 0.02 M dl-alanine, 0.02 M glycine, 0.02 M dl-lysine HCl, 0.02 M dl-serine, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 4.2→75.48 Å / Num. obs: 11894 / % possible obs: 95.8 % / Redundancy: 4 % / Biso Wilson estimate: 157.81 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.093 / Rrim(I) all: 0.202 / Χ2: 1.01 / Net I/σ(I): 5.6
Reflection shellResolution: 4.2→4.7 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3352 / CC1/2: 0.552 / Rpim(I) all: 0.499 / Rrim(I) all: 1.092 / Χ2: 1.02 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GAS

6gas


Resolution: 4.2→75.48 Å / SU ML: 0.6695 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.2221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3083 620 5.23 %
Rwork0.2268 11227 -
obs0.2312 11847 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 185.98 Å2
Refinement stepCycle: LAST / Resolution: 4.2→75.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9995 0 106 0 10101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003510307
X-RAY DIFFRACTIONf_angle_d0.742913961
X-RAY DIFFRACTIONf_chiral_restr0.05281558
X-RAY DIFFRACTIONf_plane_restr0.00491788
X-RAY DIFFRACTIONf_dihedral_angle_d12.82683803
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS7.87300503304
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.948014371596
ens_1d_4DX-RAY DIFFRACTIONTorsion NCS7.80171967634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.620.36161440.3082766X-RAY DIFFRACTION95.35
4.62-5.290.39041610.28732794X-RAY DIFFRACTION95.29
5.29-6.670.33211310.28322840X-RAY DIFFRACTION94.8
6.67-75.480.2631840.16272827X-RAY DIFFRACTION91.91

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