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- PDB-6ruz: NADH-dependent Coenzyme A Disulfide Reductase -

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Basic information

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


Oxidoreductases; Acting on NADH or NADPH / oxidoreductase activity / nucleotide binding
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 ...: / 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 / 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 29, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)197,89112
Polymers191,6794
Non-polymers6,2128
Water1,02757
1
A: NADH oxidase
B: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9466
Polymers95,8392
Non-polymers3,1064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-52 kcal/mol
Surface area32890 Å2
MethodPISA
2
C: NADH oxidase
hetero molecules

D: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9466
Polymers95,8392
Non-polymers3,1064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area11130 Å2
ΔGint-54 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.980, 159.980, 256.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-614-

HOH

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-COA / COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.28 Å3/Da / Density % sol: 71.24 %
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: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.9→58.4 Å / Num. obs: 72881 / % possible obs: 98.2 % / Redundancy: 4.41 % / Rsym value: 0.3 / Net I/σ(I): 5.58
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1.24 / Num. unique obs: 7252 / Rsym value: 2.129 / % possible all: 99.3

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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→58.38 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.38
RfactorNum. reflection% reflection
Rfree0.2439 2000 2.74 %
Rwork0.2069 --
obs0.2079 72873 98.18 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 48.066 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8799 Å20 Å2-0 Å2
2--1.8799 Å2-0 Å2
3----3.7597 Å2
Refinement stepCycle: LAST / Resolution: 2.9→58.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13513 0 404 57 13974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03414237
X-RAY DIFFRACTIONf_angle_d2.90319396
X-RAY DIFFRACTIONf_dihedral_angle_d23.3365211
X-RAY DIFFRACTIONf_chiral_restr0.172146
X-RAY DIFFRACTIONf_plane_restr0.0122473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3480X-RAY DIFFRACTIONPOSITIONAL
12B3480X-RAY DIFFRACTIONPOSITIONAL0.165
13C3478X-RAY DIFFRACTIONPOSITIONAL0.165
14D3478X-RAY DIFFRACTIONPOSITIONAL0.165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97250.3991420.35915052X-RAY DIFFRACTION99
2.9725-3.05290.4061420.3415015X-RAY DIFFRACTION99
3.0529-3.14270.3861430.31275044X-RAY DIFFRACTION99
3.1427-3.24410.29151400.28494990X-RAY DIFFRACTION99
3.2441-3.36010.3341430.26925028X-RAY DIFFRACTION99
3.3601-3.49460.33051410.25325031X-RAY DIFFRACTION99
3.4946-3.65360.2931420.23075034X-RAY DIFFRACTION98
3.6536-3.84620.24671420.20525028X-RAY DIFFRACTION99
3.8462-4.08710.23591430.18755065X-RAY DIFFRACTION99
4.0871-4.40260.18681420.16225043X-RAY DIFFRACTION98
4.4026-4.84540.19811430.14935060X-RAY DIFFRACTION98
4.8454-5.54610.19521440.17635095X-RAY DIFFRACTION98
5.5461-6.98560.23181440.19235113X-RAY DIFFRACTION97
6.9856-58.39220.20461490.18745275X-RAY DIFFRACTION96

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