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- PDB-8c3m: Crystal structure of ferredoxin/flavodoxin NADP+ oxidoreductase 1... -

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Basic information

Entry
Database: PDB / ID: 8c3m
TitleCrystal structure of ferredoxin/flavodoxin NADP+ oxidoreductase 1 (FNR1) V329H 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 / NADP binding / flavin adenine dinucleotide 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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / OXAMIC ACID / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDahlen, S.A.B. / 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 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Refinement description / Category: struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,3327
Polymers77,5242
Non-polymers1,8085
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-51 kcal/mol
Surface area29960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.612, 56.935, 94.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-530-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 39 or resid 41...
d_2ens_1(chain "B" and (resid 4 through 39 or resid 41...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUPROPROAA4 - 394 - 39
d_12LEULEUPROPROAA41 - 6141 - 61
d_13THRTHRILEILEAA63 - 9263 - 92
d_14ASNASNGLUGLUAA94 - 32594 - 325
d_15GLYGLYLYSLYSAA327 - 349327 - 349
d_16FADFADFADFADAC401
d_21GLUGLUPROPROBB4 - 394 - 39
d_22LEULEUPROPROBB41 - 6141 - 61
d_23THRTHRILEILEBB63 - 9263 - 92
d_24ASNASNGLUGLUBB94 - 32594 - 325
d_25GLYGLYLYSLYSBB327 - 349327 - 349
d_26FADFADFADFADBE401

NCS oper: (Code: givenMatrix: (0.996803490373, 0.0770279274114, -0.0212014145551), (0.0774139282122, -0.996835994484, 0.0180300809783), (-0.0197455133936, -0.0196137324352, -0.999612633074)Vector: -2. ...NCS oper: (Code: given
Matrix: (0.996803490373, 0.0770279274114, -0.0212014145551), (0.0774139282122, -0.996835994484, 0.0180300809783), (-0.0197455133936, -0.0196137324352, -0.999612633074)
Vector: -2.69248081016, 56.9910526665, -46.8187576612)

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Components

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


Mass: 38761.805 Da / Num. of mol.: 2 / Mutation: V329H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_0385 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q81IK1, 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
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 42 mg/mL protein (1:1) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0. ...Details: 42 mg/mL protein (1:1) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M MOPS/HEPES-Na pH 7.5

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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: 2.6→53.81 Å / Num. obs: 26835 / % possible obs: 96.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 55.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.049 / Rrim(I) all: 0.1 / Χ2: 1.03 / Net I/σ(I): 8.7
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3269 / CC1/2: 0.848 / Rpim(I) all: 0.281 / Rrim(I) all: 0.575 / Χ2: 1.02 / % possible all: 97.6

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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: 6GAR

6gar


Resolution: 2.6→53.81 Å / SU ML: 0.3286 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2381 1343 5.02 %
Rwork0.1878 25425 -
obs0.1903 26768 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.86 Å2
Refinement stepCycle: LAST / Resolution: 2.6→53.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5402 0 122 59 5583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845677
X-RAY DIFFRACTIONf_angle_d0.98097690
X-RAY DIFFRACTIONf_chiral_restr0.0598851
X-RAY DIFFRACTIONf_plane_restr0.0065982
X-RAY DIFFRACTIONf_dihedral_angle_d15.30912061
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.700431487902 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.32331280.29562527X-RAY DIFFRACTION96.86
2.69-2.80.31231480.26342541X-RAY DIFFRACTION98.07
2.8-2.930.28271350.2472547X-RAY DIFFRACTION97.56
2.93-3.080.29561450.24362558X-RAY DIFFRACTION96.95
3.08-3.280.28891300.23752541X-RAY DIFFRACTION96.18
3.28-3.530.27851320.19462537X-RAY DIFFRACTION95.22
3.53-3.880.20771280.16772559X-RAY DIFFRACTION96.24
3.88-4.450.22441260.15112541X-RAY DIFFRACTION94.41
4.45-5.60.19761490.1562491X-RAY DIFFRACTION92.89
5.6-53.810.20821220.17222583X-RAY DIFFRACTION89.75
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)
13.30456339983-1.040983084240.5991212738733.14307357489-0.2847516179652.87773943769-0.109397389596-0.344014003945-0.3743893667290.2437600878720.1763128085460.3786523332780.334189957254-0.320259410219-0.08242903736240.405881998367-0.04763074089330.0661774981610.4064500522910.03528299204090.503223949643-20.420148983815.9762696614-11.2048073177
24.44637819672-4.07769616281-1.142878097194.892245150761.695551709864.1890287415-0.457457476874-0.799496195477-0.07693499470541.222551938980.1591364461410.718786350527-0.278592075267-0.5977925276890.2089665686620.8681436877950.038631786090.2088653198860.877467094917-0.1203741411450.86697016151-33.66478673338.1884512997.35915143801
34.854812260490.3287597048571.810999238632.631787490080.4994460207793.76563345304-0.101960864308-0.0420539396126-0.139712788739-0.176772076476-0.026607949930.1189178866620.290197968303-0.124448706550.09506866033380.3756765844460.009135224019920.08037823032350.3313703482690.0471518924820.495035907557-14.752684584618.2433885562-19.7899848944
42.53353398220.2492668822780.3848007304263.292506524750.04351054060721.78992454425-0.1514276529990.2900114064210.421749508346-0.434728137359-0.001752646022170.18345422162-0.30127592467-0.1356000317280.1673957545880.424360582510.0438574910787-0.08805534194830.4062845085310.04546735630980.543511995237-22.880080320937.3580675986-38.505704195
53.152606193783.087782073430.2333765765026.27682838333-0.07360911161538.923581450120.08682038864210.27866614881-0.337939680211-0.2229245331450.46593373295-0.1629555939710.05524774330750.144060336528-0.4904730249020.571783084210.0379079549384-0.1904247946720.574208020357-0.1357467846160.704589888132-35.940249317815.3364695729-48.4979359292
67.923327920190.351222060277-1.877190076648.84204891133-0.9179796183986.2023704358-0.4356884930011.38663965589-0.678204637799-1.075837816560.074955773871-0.1152937736890.4032872457480.2272689977480.3260695097361.03114556321-0.0443619592113-0.1573355492140.819491040755-0.2411605015170.757682692085-34.115602783111.5050988011-58.7998397568
73.859183363371.202872346981.694616055452.412571629480.7999664797581.92299661403-0.1514702626140.46882366099-0.0404439281084-0.3440461830240.06730329454960.0475343725743-0.2043100085550.1780388005860.06333652308580.4275319744060.00873140040401-0.0007953123151420.408942963130.01844165311240.461185490571-13.714431379531.4409971568-37.8479120189
89.132804133413.05851662887-0.3864525932376.2536551537-0.4445566973785.509105504940.00598185755595-1.828849655451.084725127560.176017750356-0.2683505331740.816488664472-0.863552194162-0.9102037169360.2000011727610.7135287494740.212297543393-0.1387868008910.770548724031-0.2272670129370.725404225791-28.826031223442.8457718566-15.4951293029
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 116 )AA4 - 1161 - 113
22chain 'A' and (resid 117 through 253 )AA117 - 253114 - 250
33chain 'A' and (resid 254 through 349 )AA254 - 349251 - 346
44chain 'B' and (resid 4 through 138 )BD4 - 1381 - 135
55chain 'B' and (resid 139 through 183 )BD139 - 183136 - 180
66chain 'B' and (resid 184 through 237 )BD184 - 237181 - 234
77chain 'B' and (resid 238 through 319 )BD238 - 319235 - 316
88chain 'B' and (resid 320 through 349 )BD320 - 349317 - 346

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