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

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Basic information

Entry
Database: PDB / ID: 5kmr
TitleThe structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 3.0 angstrom resolution.
ComponentsFAD-dependent pyridine nucleotide-disulfide oxidoreductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / NADH DEHYDROGENASE
Function / homology
Function and homology information


oxidoreductase 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: 3 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 1.0Jan 25, 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
B: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
A: 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)183,42011
Polymers178,2884
Non-polymers5,1327
Water30617
1
B: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
A: 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 area5880 Å2
ΔGint-21 kcal/mol
Surface area31580 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)92,0426
Polymers89,1442
Non-polymers2,8984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-24 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.061, 114.206, 130.957
Angle α, β, γ (deg.)90.00, 91.53, 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 / 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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.1 Å3/Da / Density % sol: 60.38 %
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 10mM NAD+

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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 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3→47.8 Å / Num. obs: 42174 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 66.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

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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: 3→43.637 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3
RfactorNum. reflection% reflection
Rfree0.2542 2134 5.06 %
Rwork0.2373 --
obs0.2382 42151 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→43.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11107 0 344 17 11468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211700
X-RAY DIFFRACTIONf_angle_d0.72416071
X-RAY DIFFRACTIONf_dihedral_angle_d13.0143824
X-RAY DIFFRACTIONf_chiral_restr0.031915
X-RAY DIFFRACTIONf_plane_restr0.0052044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.06980.37421590.35212623X-RAY DIFFRACTION100
3.0698-3.14660.35781410.33432700X-RAY DIFFRACTION100
3.1466-3.23160.33851480.32072636X-RAY DIFFRACTION100
3.2316-3.32670.35071350.32672X-RAY DIFFRACTION99
3.3267-3.4340.3281280.30252707X-RAY DIFFRACTION100
3.434-3.55670.29161340.28082674X-RAY DIFFRACTION99
3.5567-3.6990.27411350.25762660X-RAY DIFFRACTION99
3.699-3.86730.28811190.25832703X-RAY DIFFRACTION99
3.8673-4.0710.29021280.24152695X-RAY DIFFRACTION99
4.071-4.32590.24061220.23312675X-RAY DIFFRACTION99
4.3259-4.65950.23741350.21222683X-RAY DIFFRACTION99
4.6595-5.12780.22921460.21472661X-RAY DIFFRACTION99
5.1278-5.86830.24131650.22942636X-RAY DIFFRACTION98
5.8683-7.38760.2511520.21482653X-RAY DIFFRACTION98
7.3876-43.64140.18651870.17752639X-RAY DIFFRACTION97

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