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

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Basic information

Entry
Database: PDB / ID: 6rvh
TitleNADH-dependent Coenzyme A Disulfide Reductase soaked with Menadione
ComponentsNADH oxidase
KeywordsOXIDOREDUCTASE / Coenzyme A Disulfide Reductase / NADH oxidation / flavoprotein / Menadione
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 / MENADIONE / NADH oxidase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
Revision 1.3Nov 20, 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)198,58016
Polymers191,6794
Non-polymers6,90112
Water2,450136
1
A: NADH oxidase
B: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2908
Polymers95,8392
Non-polymers3,4516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-59 kcal/mol
Surface area31890 Å2
MethodPISA
2
C: NADH oxidase
hetero molecules

D: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2908
Polymers95,8392
Non-polymers3,4516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area12220 Å2
ΔGint-61 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.950, 159.950, 255.930
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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-VK3 / MENADIONE / VITAMIN K3 / 2-METHYL-1,4-NAPHTHALENEDIONE


Mass: 172.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 4.27 Å3/Da / Density % sol: 71.19 %
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: 3→58.4 Å / Num. obs: 63717 / % possible obs: 95 % / Redundancy: 3.01 % / Rsym value: 0.294 / Net I/σ(I): 4.37
Reflection shellResolution: 3→3.1 Å / Mean I/σ(I) obs: 1.25 / Num. unique obs: 6095 / Rsym value: 1.344

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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: 3→58.346 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.45
RfactorNum. reflection% reflection
Rfree0.2588 2000 3.14 %
Rwork0.2149 --
obs0.2163 63708 94.97 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 26.688 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2832 Å20 Å20 Å2
2--0.2832 Å20 Å2
3----0.5665 Å2
Refinement stepCycle: LAST / Resolution: 3→58.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13513 0 456 136 14105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03414293
X-RAY DIFFRACTIONf_angle_d2.96719476
X-RAY DIFFRACTIONf_dihedral_angle_d22.5615211
X-RAY DIFFRACTIONf_chiral_restr0.1672146
X-RAY DIFFRACTIONf_plane_restr0.0112477
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3493X-RAY DIFFRACTIONPOSITIONAL
12B3493X-RAY DIFFRACTIONPOSITIONAL0.174
13C3491X-RAY DIFFRACTIONPOSITIONAL0.17
14D3491X-RAY DIFFRACTIONPOSITIONAL0.188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.07510.40631440.35184443X-RAY DIFFRACTION97
3.0751-3.15820.40741420.34144377X-RAY DIFFRACTION97
3.1582-3.25110.34461430.30324412X-RAY DIFFRACTION96
3.2511-3.35610.33921410.29394355X-RAY DIFFRACTION95
3.3561-3.4760.33751430.27624391X-RAY DIFFRACTION96
3.476-3.61510.31871420.25424410X-RAY DIFFRACTION96
3.6151-3.77960.27371440.22944451X-RAY DIFFRACTION96
3.7796-3.97890.21561430.19924420X-RAY DIFFRACTION96
3.9789-4.22810.22441400.1964299X-RAY DIFFRACTION93
4.2281-4.55440.2251420.16974382X-RAY DIFFRACTION95
4.5544-5.01250.23441430.17024394X-RAY DIFFRACTION95
5.0125-5.73730.25861420.18884380X-RAY DIFFRACTION94
5.7373-7.22630.1981440.17364437X-RAY DIFFRACTION93
7.2263-58.35680.18591470.17014557X-RAY DIFFRACTION91

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