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- PDB-5kmp: The structure of G164E variant of type II NADH dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 5kmp
TitleThe structure of G164E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum
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 / FAD-dependent pyridine nucleotide-disulfide oxidoreductase
Similarity search - Component
Biological speciesCaldalkalibacillus thermarum TA2.A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,8594
Polymers89,2882
Non-polymers1,5712
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-21 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.098, 93.098, 248.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 44644.051 Da / Num. of mol.: 2 / Mutation: G164E
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.: 2
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.07 Å3/Da / Density % sol: 59.87 %
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 30 mM D, L-lysine

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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: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.2→46.6 Å / Num. obs: 18732 / % possible obs: 99.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 69.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 17.8
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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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: 3.2→45.753 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.12
RfactorNum. reflection% reflection
Rfree0.2338 958 5.12 %
Rwork0.2025 --
obs0.2042 18713 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→45.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 106 4 5679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045798
X-RAY DIFFRACTIONf_angle_d0.9437956
X-RAY DIFFRACTIONf_dihedral_angle_d15.9531903
X-RAY DIFFRACTIONf_chiral_restr0.033944
X-RAY DIFFRACTIONf_plane_restr0.0081023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.36880.30691350.28012482X-RAY DIFFRACTION100
3.3688-3.57980.31041230.24672495X-RAY DIFFRACTION100
3.5798-3.85610.29531300.23242520X-RAY DIFFRACTION100
3.8561-4.24390.25451280.20682504X-RAY DIFFRACTION100
4.2439-4.85740.19951440.1812520X-RAY DIFFRACTION99
4.8574-6.11750.21191510.19832549X-RAY DIFFRACTION99
6.1175-45.75780.20561470.17452685X-RAY DIFFRACTION98

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