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- PDB-8dos: Crystal structure of Ferredoxin (flavodoxin):NADP(+) oxidoreducta... -

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Basic information

Entry
Database: PDB / ID: 8dos
TitleCrystal structure of Ferredoxin (flavodoxin):NADP(+) oxidoreductase from Klebsiella pneumoniae
ComponentsFlavodoxin/ferredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


flavodoxin-NADP+ reductase / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / nucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavodoxin/ferredoxin--NADP reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.872 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Ferredoxin (flavodoxin):NADP(+) oxidoreductase from Klebsiella pneumoniae
Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn / Item: _diffrn.ambient_temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavodoxin/ferredoxin--NADP reductase
B: Flavodoxin/ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,50911
Polymers57,8702
Non-polymers3,6399
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-43 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.240, 56.020, 56.110
Angle α, β, γ (deg.)106.690, 97.490, 83.400
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Flavodoxin/ferredoxin--NADP reductase / Ferredoxin (flavodoxin):NADP(+) oxidoreductase / Ferredoxin--NADP reductase / Flavodoxin--NADP reductase


Mass: 28935.129 Da / Num. of mol.: 2 / Fragment: KlpnC.00101.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: fpr, BL124_00025130, DRB11_17480, EAO17_13200, G7Z27_00550, GJJ08_000550, GNE24_19530, GNG14_18110, SAMEA3499874_03593, SAMEA3500057_03748, SAMEA3649758_03020, SAMEA3720909_02704, SAMEA3727679_03443, KPHS_29700
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0G3NED2, ferredoxin-NADP+ reductase, flavodoxin-NADP+ reductase

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Non-polymers , 6 types, 429 molecules

#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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus A9: 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000, 100 mM Tris/BICINE, 30 mM MgCl2 and 30 mM CaCl2, KlpnC.00101.a.B1.PS38694 at 21.7 mg/mL, Tray: plate 12372 well A9 dro 2, Puck: PSL1202, Cryo: DIRECT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 24, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.872→53.481 Å / Num. obs: 42132 / % possible obs: 93.9 % / Redundancy: 2 % / Biso Wilson estimate: 15.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.07 / Rrim(I) all: 0.102 / Net I/σ(I): 7.9 / Num. measured all: 82827
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.872-1.9040.326390620380.7940.310.4512.291.5
5.081-53.4810.031411521250.9960.0290.04219.994.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX0.97949refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 0.97949 / Resolution: 1.872→27.37 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 2045 4.86 %
Rwork0.1706 40073 -
obs0.1723 42118 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.4 Å2 / Biso mean: 18.8496 Å2 / Biso min: 8.02 Å2
Refinement stepCycle: final / Resolution: 1.872→27.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 237 420 4512
Biso mean--23.78 26.77 -
Num. residues----493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.872-1.920.26921380.2167258892
1.92-1.960.26331350.1979272394
1.96-2.020.24631520.1826263994
2.02-2.080.22331130.1818271893
2.08-2.140.20841170.1778268594
2.14-2.220.23251120.1736266593
2.22-2.310.22791340.1686260192
2.31-2.410.2011260.1676253889
2.41-2.540.21791300.1667275796
2.54-2.70.22051310.1725271596
2.7-2.910.20181560.1699272395
2.91-3.20.19641410.1679266795
3.2-3.660.20731360.1592264392
3.66-4.610.161680.1454272497
4.61-27.370.19191560.1858268795
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)
11.6591-0.079-0.78383.6112-0.07461.2473-0.00010.05270.058-0.12940.0007-0.0671-0.00330.06360.01050.0926-0.0129-0.00470.0889-0.00340.0372-5.393310.4424-34.6137
25.06641.12140.06292.7783-1.19753.97560.0889-0.2380.13230.07670.0059-0.37450.03210.3484-0.03850.07710.0170.01050.144-0.03260.14131.665112.8456-25.6991
32.22010.0267-0.21742.6397-0.10912.0953-0.0307-0.0260.1336-0.1221-0.05020.0012-0.0980.08660.06760.08170.0029-0.00090.07030.0060.0667-4.773813.73-32.5129
45.16033.2979-2.72242.3334-1.70742.2066-0.2233-0.0597-0.3957-0.0303-0.0007-0.16330.33650.09660.21870.15530.01610.01920.0855-0.01220.1074-14.3843-3.7935-22.1323
51.5413-0.0788-0.35292.24080.38041.6608-0.0050.11230.11660.0114-0.00830.13680.0215-0.11760.02170.06060.0042-0.00050.10440.01210.0925-25.37529.1579-27.2084
63.3685-1.22710.922.92740.5871.72320.0349-0.0213-0.09580.22980.11990.4265-0.007-0.2631-0.14930.0677-0.0130.05090.17450.04470.1529-34.46214.5626-17.2839
72.84092.018-0.60572.3415-0.50330.28440.1524-0.21720.08750.1964-0.11280.1192-0.1350.104-0.04370.1644-0.01750.03540.1023-0.01230.1016-22.28998.2646-11.9687
81.3951.7761-0.05575.3612-1.77022.05180.1307-0.2413-0.03860.1266-0.0811-0.20830.02840.1138-0.02450.1467-0.02080.00420.1407-0.01140.0894-16.66440.6731-11.8527
96.48270.9321-4.46313.58840.35515.44950.078-0.04110.4143-0.00180.0190.0709-0.1496-0.0923-0.10610.10770.0192-0.04260.08740.03030.0531-19.336742.5262-1.6615
102.1913-0.5836-0.63142.252-0.39412.3490.1153-0.05240.1586-0.03020.00360.0669-0.0865-0.0317-0.13640.0945-0.004-0.00030.0573-0.0110.0929-14.814637.30331.4888
116.616-2.22261.47144.5353-0.32245.73680.0560.32280.252-0.5030.04960.43880.044-0.3567-0.11170.1596-0.0501-0.02230.13150.0240.1356-24.589132.973-5.7151
122.0356-0.4309-0.36231.7106-0.33451.8704-0.02280.10280.0188-0.11570.01420.04760.0041-0.02020.00620.1072-0.0221-0.00080.07360.00930.0719-17.180738.0366-2.8098
135.2519-5.39324.14756.5064-4.24793.6442-0.1155-0.2841-0.19660.25330.17840.30880.1099-0.2268-0.05850.1612-0.02030.02180.1209-0.02560.0866-13.830721.608411.7555
141.9203-0.3763-0.41692.04550.40011.2724-0.0635-0.12360.03850.20220.0859-0.1240.05440.2177-0.03330.13620.00180.00370.0777-0.00930.0942-4.059825.63158.257
150.9657-0.814-0.34141.0258-1.40398.5698-0.03810.04350.14770.00040.0786-0.2704-0.29710.3543-0.04110.1159-0.05160.02550.1012-0.00510.16611.486633.91811.6404
161.74730.3464-0.30992.0259-0.49712.6288-0.1170.1535-0.1502-0.19460.0619-0.39620.13610.16970.05780.085-0.00050.01540.1303-0.01020.17185.639319.7867-0.1095
171.45-0.90372.11250.9353-1.5434.7270.0593-0.0151-0.1157-0.0565-0.00670.04710.12930.0581-0.05450.1636-0.00790.03020.0922-0.00310.0959-5.692813.0829-1.282
180.87210.17131.01882.7183-2.64914.51360.1540.0097-0.1270.0307-0.04250.21330.0934-0.2482-0.09020.1688-0.01080.02590.1095-0.010.1049-12.081913.11474.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )A2 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 53 )A36 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 91 )A54 - 91
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 107 )A92 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 190 )A108 - 190
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 206 )A191 - 206
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 229 )A207 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 248 )A230 - 248
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 14 )B3 - 14
10X-RAY DIFFRACTION10chain 'B' and (resid 15 through 35 )B15 - 35
11X-RAY DIFFRACTION11chain 'B' and (resid 36 through 53 )B36 - 53
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 91 )B54 - 91
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 107 )B92 - 107
14X-RAY DIFFRACTION14chain 'B' and (resid 108 through 143 )B108 - 143
15X-RAY DIFFRACTION15chain 'B' and (resid 144 through 162 )B144 - 162
16X-RAY DIFFRACTION16chain 'B' and (resid 163 through 206 )B163 - 206
17X-RAY DIFFRACTION17chain 'B' and (resid 207 through 229 )B207 - 229
18X-RAY DIFFRACTION18chain 'B' and (resid 230 through 248 )B230 - 248

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