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- PDB-5kms: The structure of type II NADH dehydrogenase from Caldalkalibacill... -

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Basic information

Entry
Database: PDB / ID: 5kms
TitleThe structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 angstrom resolution.
ComponentsFAD-dependent pyridine nucleotide-disulfide oxidoreductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / NADH DEHYDROGENASE
Function / homology
Function and homology information


aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / nucleotide binding
Similarity search - Function
: / FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / FAD-dependent pyridine nucleotide-disulfide oxidoreductase
Similarity search - Component
Biological speciesCaldalkalibacillus thermarum TA2.A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCook, G.M. / Aragao, D. / Nakatani, Y.
CitationJournal: Sci Rep / Year: 2017
Title: The mechanism of catalysis by type-II NADH:quinone oxidoreductases.
Authors: Blaza, J.N. / Bridges, H.R. / Aragao, D. / Dunn, E.A. / Heikal, A. / Cook, G.M. / Nakatani, Y. / Hirst, J.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / diffrn_source
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
B: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
C: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
D: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,0949
Polymers178,2884
Non-polymers3,8065
Water3,873215
1
A: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
B: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3795
Polymers89,1442
Non-polymers2,2353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-20 kcal/mol
Surface area32030 Å2
MethodPISA
2
C: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
D: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7154
Polymers89,1442
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-20 kcal/mol
Surface area32430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.883, 114.014, 130.638
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FAD-dependent pyridine nucleotide-disulfide oxidoreductase


Mass: 44571.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: CathTA2_0279 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: F5L3B8
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bicine/Tris buffer pH8.5 including 10% (v/v) PEG 4000, 25% (v/v) ethylene glycol and 1mM NADH

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→47.9 Å / Num. obs: 73912 / % possible obs: 99.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.508 / Mean I/σ(I) obs: 1.7 / Num. unique all: 42902 / CC1/2: 0.613 / % possible all: 99.3

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Processing

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

4nwz


Resolution: 2.5→47.89 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.16
RfactorNum. reflection% reflection
Rfree0.244 3725 5.04 %
Rwork0.214 --
obs0.216 73869 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11498 0 256 215 11969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312004
X-RAY DIFFRACTIONf_angle_d0.74416429
X-RAY DIFFRACTIONf_dihedral_angle_d14.6654089
X-RAY DIFFRACTIONf_chiral_restr0.0291927
X-RAY DIFFRACTIONf_plane_restr0.0052096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53170.37831370.31332574X-RAY DIFFRACTION99
2.5317-2.5650.3591230.30912591X-RAY DIFFRACTION100
2.565-2.60010.35011070.28662654X-RAY DIFFRACTION100
2.6001-2.63730.30941180.28632582X-RAY DIFFRACTION100
2.6373-2.67660.3681390.28412569X-RAY DIFFRACTION100
2.6766-2.71840.31621140.27432636X-RAY DIFFRACTION100
2.7184-2.7630.34161310.28362585X-RAY DIFFRACTION100
2.763-2.81060.31220.27322598X-RAY DIFFRACTION100
2.8106-2.86170.30631370.28542568X-RAY DIFFRACTION100
2.8617-2.91680.32291330.26532644X-RAY DIFFRACTION100
2.9168-2.97630.29881340.26792556X-RAY DIFFRACTION100
2.9763-3.0410.31861280.27252628X-RAY DIFFRACTION100
3.041-3.11170.34211310.25622589X-RAY DIFFRACTION100
3.1117-3.18950.29221390.2472575X-RAY DIFFRACTION100
3.1895-3.27580.28481300.24412597X-RAY DIFFRACTION100
3.2758-3.37210.25791660.23812574X-RAY DIFFRACTION100
3.3721-3.48090.25861410.232603X-RAY DIFFRACTION100
3.4809-3.60530.24211370.2192597X-RAY DIFFRACTION100
3.6053-3.74960.25341430.21192582X-RAY DIFFRACTION100
3.7496-3.92020.23781690.20452554X-RAY DIFFRACTION100
3.9202-4.12680.21991470.19692608X-RAY DIFFRACTION100
4.1268-4.38510.20491420.18672605X-RAY DIFFRACTION100
4.3851-4.72350.19591580.17122575X-RAY DIFFRACTION100
4.7235-5.19830.23351390.17522636X-RAY DIFFRACTION100
5.1983-5.94930.18531580.19532587X-RAY DIFFRACTION100
5.9493-7.49080.22371550.18682618X-RAY DIFFRACTION100
7.4908-47.90070.18161470.1642659X-RAY DIFFRACTION99

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