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- PDB-6rvb: NADH-dependent Coenzyme A Disulfide Reductase soaked with NADH -

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Basic information

Entry
Database: PDB / ID: 6rvb
TitleNADH-dependent Coenzyme A Disulfide Reductase soaked with NADH
ComponentsNADH oxidase
KeywordsOXIDOREDUCTASE / Coenzyme A Disulfide Reductase / NADH:menaquinone Oxidoreductase / flavoprotein
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH / flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH oxidase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKoepke, J. / Preu, J.
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2019
Title: Characterization and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus.
Authors: Lencina, A.M. / Koepke, J. / Preu, J. / Muenke, C. / Gennis, R.B. / Michel, H. / Schurig-Briccio, L.A.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 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: NADH oxidase
B: NADH oxidase
C: NADH oxidase
D: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,54516
Polymers191,6794
Non-polymers8,86612
Water2,018112
1
A: NADH oxidase
B: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2728
Polymers95,8392
Non-polymers4,4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-61 kcal/mol
Surface area32270 Å2
MethodPISA
2
C: NADH oxidase
hetero molecules

D: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2728
Polymers95,8392
Non-polymers4,4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area13540 Å2
ΔGint-61 kcal/mol
Surface area32270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.750, 160.750, 256.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B
311chain C
411chain D

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Components

#1: Protein
NADH oxidase


Mass: 47919.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_C1484 / Production host: Escherichia coli (E. coli)
References: UniProt: Q72HK3, Oxidoreductases; Acting on NADH or NADPH
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 4.33 Å3/Da / Density % sol: 71.59 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES-Na, NaCl, FAD, dodecyl-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→47.9 Å / Num. obs: 75111 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rsym value: 0.266 / Net I/σ(I): 7.31
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 7152 / Rsym value: 2.047

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nta

3nta


Resolution: 2.9→47.897 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2
RfactorNum. reflection% reflection
Rfree0.2463 2000 2.66 %
Rwork0.2008 --
obs0.2021 75095 99.95 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 46.211 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1947 Å20 Å20 Å2
2--0.1947 Å20 Å2
3----0.3893 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13513 0 580 112 14205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03214429
X-RAY DIFFRACTIONf_angle_d2.98419688
X-RAY DIFFRACTIONf_dihedral_angle_d23.3985307
X-RAY DIFFRACTIONf_chiral_restr0.1622178
X-RAY DIFFRACTIONf_plane_restr0.0122485
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3524X-RAY DIFFRACTIONPOSITIONAL
12B3524X-RAY DIFFRACTIONPOSITIONAL0.149
13C3522X-RAY DIFFRACTIONPOSITIONAL0.142
14D3522X-RAY DIFFRACTIONPOSITIONAL0.138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97250.44051420.41445166X-RAY DIFFRACTION100
2.9725-3.05290.39381390.37975096X-RAY DIFFRACTION100
3.0529-3.14270.42081410.32825152X-RAY DIFFRACTION100
3.1427-3.24410.33351400.28865151X-RAY DIFFRACTION100
3.2441-3.360.2691420.2475163X-RAY DIFFRACTION100
3.36-3.49450.27881420.21875197X-RAY DIFFRACTION100
3.4945-3.65350.27511410.22015174X-RAY DIFFRACTION100
3.6535-3.8460.27831420.20435175X-RAY DIFFRACTION100
3.846-4.08690.21921420.17145182X-RAY DIFFRACTION100
4.0869-4.40220.17361420.14165208X-RAY DIFFRACTION100
4.4022-4.84490.17791440.13095249X-RAY DIFFRACTION100
4.8449-5.5450.17451450.1555281X-RAY DIFFRACTION100
5.545-6.98270.23331450.18495334X-RAY DIFFRACTION100
6.9827-47.90390.23241530.18795567X-RAY DIFFRACTION100

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