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

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Basic information

Entry
Database: PDB / ID: 4ylf
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 / 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 / MAD / Resolution: 2.301 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 5, 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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)169,56616
Polymers164,4764
Non-polymers5,09012
Water2,882160
1
A: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog
B: Dihydropyrimidine dehydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7838
Polymers82,2382
Non-polymers2,5456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-103 kcal/mol
Surface area31030 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)84,7838
Polymers82,2382
Non-polymers2,5456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-94 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.420, 81.420, 311.480
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 (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (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 (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: THEMA_06045 / Production host: Escherichia coli bl21(de3) (bacteria) / Variant (production host): C41 / References: UniProt: V9X7T9, UniProt: Q9X1X5*PLUS

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Non-polymers , 5 types, 172 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: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NH4H2PO4

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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: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.2 Å / Num. obs: 86542 / % possible obs: 96.92 % / Redundancy: 2.9 % / Rsym value: 0.078 / Net I/σ(I): 8.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.4 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
SHARPphasing
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.301→46.294 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.11 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2189 4429 5.12 %
Rwork0.1872 --
obs0.191 86518 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→46.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11421 0 262 160 11843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811960
X-RAY DIFFRACTIONf_angle_d1.0616188
X-RAY DIFFRACTIONf_dihedral_angle_d15.2794467
X-RAY DIFFRACTIONf_chiral_restr0.0391773
X-RAY DIFFRACTIONf_plane_restr0.0052048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3007-2.34040.27792140.27433880X-RAY DIFFRACTION87
2.3404-2.38290.27221910.27394195X-RAY DIFFRACTION94
2.3829-2.42880.33352340.27184149X-RAY DIFFRACTION94
2.4288-2.47830.29542370.26934183X-RAY DIFFRACTION93
2.4783-2.53220.32642000.26154207X-RAY DIFFRACTION94
2.5322-2.59110.27792100.25994131X-RAY DIFFRACTION94
2.5911-2.65580.26462010.24644221X-RAY DIFFRACTION94
2.6558-2.72760.28792150.24414229X-RAY DIFFRACTION94
2.7276-2.80780.24262260.2314194X-RAY DIFFRACTION93
2.8078-2.89840.26882190.22334111X-RAY DIFFRACTION93
2.8984-3.00190.27232120.21934133X-RAY DIFFRACTION93
3.0019-3.1220.2612200.20954105X-RAY DIFFRACTION92
3.122-3.26390.25672470.20394143X-RAY DIFFRACTION92
3.2639-3.43580.23692200.18854088X-RAY DIFFRACTION93
3.4358-3.65080.21042140.17424103X-RAY DIFFRACTION92
3.6508-3.93220.19072330.16324006X-RAY DIFFRACTION90
3.9322-4.3270.15281920.13664056X-RAY DIFFRACTION90
4.327-4.9510.15792250.12694042X-RAY DIFFRACTION90
4.951-6.22980.17071980.16184011X-RAY DIFFRACTION90
6.2298-31.43890.18882090.16473980X-RAY DIFFRACTION88
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)
10.9336-0.34210.56260.2952-0.2630.42060.00480.10320.0012-0.03230.0326-0.0240.05010.1511-0.00220.3095-0.0355-0.34820.0736-0.09830.3379-12.226819.122341.6556
21.3248-0.06270.6761.0569-0.36871.2295-0.01340.00340.04240.0514-0.1165-0.2736-0.03670.07060.11220.19240.0249-0.05350.1494-0.05540.4322-32.314918.72510.1031
30.7256-0.12910.21940.4683-0.18821.1179-0.05820.09280.0473-0.4780.04050.32970.0046-0.25990.04590.73150.0592-0.58410.367-0.09390.8504-27.075260.364238.1893
41.34680.00250.59030.66850.07091.3174-0.0194-0.0203-0.0117-0.0795-0.08130.276-0.0279-0.06250.12210.2167-0.0393-0.08560.16290.03690.4401-8.270259.312269.3968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 502 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 503 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 502)
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 503)

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