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- PDB-4yry: Insights into flavin-based electron bifurcation via the NADH-depe... -

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Basic information

Entry
Database: PDB / ID: 4yry
TitleInsights into flavin-based electron bifurcation via the NADH-dependent reduced ferredoxin-NADP oxidoreductase structure
Components
  • Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog
  • Dihydropyrimidine dehydrogenase subunit A
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


pyrimidine nucleotide biosynthetic process / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Glutamate synthase (NADPH), homotetrameric / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Alpha-helical ferredoxin / FAD/NAD(P)-binding domain ...Glutamate synthase (NADPH), homotetrameric / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Alpha-helical ferredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / IRON/SULFUR CLUSTER / Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog / Glutamate synthase, beta subunit / :
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsErmler, U. / Thauer, R.K. / Demmer, J.K. / Huang, H. / Wang, S. / Demmer, U.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Insights into Flavin-based Electron Bifurcation via the NADH-dependent Reduced Ferredoxin:NADP Oxidoreductase Structure.
Authors: Demmer, J.K. / Huang, H. / Wang, S. / Demmer, U. / Thauer, R.K. / Ermler, U.
History
DepositionMar 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 21, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.4Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog
B: Dihydropyrimidine dehydrogenase subunit A
C: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog
D: Dihydropyrimidine dehydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,79817
Polymers164,4764
Non-polymers6,32213
Water2,378132
1
A: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog
B: Dihydropyrimidine dehydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3518
Polymers82,2382
Non-polymers3,1146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-95 kcal/mol
Surface area30040 Å2
MethodPISA
2
C: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog
D: Dihydropyrimidine dehydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4469
Polymers82,2382
Non-polymers3,2097
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-94 kcal/mol
Surface area31680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.400, 81.400, 307.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog / Dihydroorotate oxidase B / electron transfer subunit homolog


Mass: 30555.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1639 / Plasmid: pET-51b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9X1X4
#2: Protein Dihydropyrimidine dehydrogenase subunit A /


Mass: 51682.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: THEMA_06045 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: V9X7T9, UniProt: Q9X1X5*PLUS

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Non-polymers , 6 types, 145 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.225M NH4H2PO4, 5 % (v,v) Ethanol, 20 % glycerol. soaked for 40 min in 5 mM NADH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2013
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: 76947 / % possible obs: 99.1 % / Redundancy: 5.2 % / Rsym value: 0.113 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.896 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLF

4ylf


Resolution: 2.4→19.96 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2491 3787 4.94 %
Rwork0.1996 --
obs0.2039 76728 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11439 0 345 132 11916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512068
X-RAY DIFFRACTIONf_angle_d0.90916347
X-RAY DIFFRACTIONf_dihedral_angle_d15.3134474
X-RAY DIFFRACTIONf_chiral_restr0.0341793
X-RAY DIFFRACTIONf_plane_restr0.0032057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4014-2.44270.41251680.30833523X-RAY DIFFRACTION92
2.4427-2.4870.35042060.29193573X-RAY DIFFRACTION92
2.487-2.53470.37241760.28083667X-RAY DIFFRACTION95
2.5347-2.58640.34051640.27993632X-RAY DIFFRACTION95
2.5864-2.64250.29691860.28323701X-RAY DIFFRACTION95
2.6425-2.70380.30251950.27023649X-RAY DIFFRACTION95
2.7038-2.77120.2691850.25643649X-RAY DIFFRACTION95
2.7712-2.84590.31051820.25423671X-RAY DIFFRACTION95
2.8459-2.92940.27072170.23873639X-RAY DIFFRACTION94
2.9294-3.02360.29891820.22913696X-RAY DIFFRACTION95
3.0236-3.13120.30721860.22653666X-RAY DIFFRACTION95
3.1312-3.2560.2772240.21893624X-RAY DIFFRACTION94
3.256-3.40340.26441840.2043627X-RAY DIFFRACTION95
3.4034-3.58180.23551770.19573657X-RAY DIFFRACTION94
3.5818-3.80460.25471800.1933638X-RAY DIFFRACTION95
3.8046-4.09580.21541900.17093655X-RAY DIFFRACTION94
4.0958-4.50330.2341920.15023641X-RAY DIFFRACTION94
4.5033-5.14410.18681790.15353640X-RAY DIFFRACTION94
5.1441-6.44090.21851990.17963653X-RAY DIFFRACTION94
6.4409-19.320.17921750.16213673X-RAY DIFFRACTION94
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)
10.47810.46040.13811.39060.9560.65150.00020.03870.1792-0.0146-0.03420.119-0.06180.03580.09770.59290.0006-0.29560.4646-0.07380.3335-19.662639.876539.9793
20.30150.45450.48370.46990.74641.1321-0.0372-0.00670.016-0.0074-0.07850.0346-0.0364-0.01030.07670.38280.0653-0.10760.35850.02980.2653-20.199539.416839.7848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and (resid 1 through 276 )) or (chain 'C' and (resid 1 through 276 ))
2X-RAY DIFFRACTION2(chain 'B' and (resid 1 through 468 )) or (chain 'D' and (resid 1 through 468 ))

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