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- PDB-5kmq: The structure of I379E variant of type II NADH dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 5kmq
TitleThe structure of I379E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum
ComponentsFAD-dependent pyridine nucleotide-disulfide oxidoreductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / NADH DEHYDROGENASE / I379E mutation
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 / FAD-dependent pyridine nucleotide-disulfide oxidoreductase
Similarity search - Component
Biological speciesCaldalkalibacillus thermarum TA2.A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCook, G.M. / Aragao, D. / Nakatani, Y.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council and Maurice Wilkins Centre New Zealand
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
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)181,4948
Polymers178,3524
Non-polymers3,1424
Water1,31573
1
A: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
B: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7474
Polymers89,1762
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-19 kcal/mol
Surface area32150 Å2
2
C: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
D: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7474
Polymers89,1762
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-17 kcal/mol
Surface area31610 Å2
Unit cell
Length a, b, c (Å)72.383, 114.366, 130.462
Angle α, β, γ (deg.)90.00, 92.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44587.945 Da / Num. of mol.: 4 / Mutation: I379E
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: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
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 55mM 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: Oct 18, 2015
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.7→47.6 Å / Num. obs: 56903 / % possible obs: 97.4 % / Redundancy: 3 % / Biso Wilson estimate: 52.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 11.6
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.6 / % 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: 2.7→44.859 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2
RfactorNum. reflection% reflection
Rfree0.2692 2806 4.93 %
Rwork0.223 --
obs0.2252 56890 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11049 0 212 73 11334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611497
X-RAY DIFFRACTIONf_angle_d1.05215762
X-RAY DIFFRACTIONf_dihedral_angle_d14.8393798
X-RAY DIFFRACTIONf_chiral_restr0.0411855
X-RAY DIFFRACTIONf_plane_restr0.0072041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74660.39591530.35392723X-RAY DIFFRACTION99
2.7466-2.79650.40221420.32092790X-RAY DIFFRACTION99
2.7965-2.85030.36321430.33042697X-RAY DIFFRACTION99
2.8503-2.90840.41071500.30852750X-RAY DIFFRACTION99
2.9084-2.97170.33791540.28932742X-RAY DIFFRACTION100
2.9717-3.04080.37371190.29172775X-RAY DIFFRACTION100
3.0408-3.11680.32371310.27952769X-RAY DIFFRACTION99
3.1168-3.20110.32311630.27662719X-RAY DIFFRACTION99
3.2011-3.29520.28281410.25052758X-RAY DIFFRACTION99
3.2952-3.40150.23561200.23542736X-RAY DIFFRACTION99
3.4015-3.52310.31461500.23372727X-RAY DIFFRACTION98
3.5231-3.66410.24821310.22052742X-RAY DIFFRACTION98
3.6641-3.83070.28751540.22042697X-RAY DIFFRACTION98
3.8307-4.03260.26431500.21852710X-RAY DIFFRACTION98
4.0326-4.28510.24921310.19862676X-RAY DIFFRACTION97
4.2851-4.61560.20961570.18512653X-RAY DIFFRACTION96
4.6156-5.07950.23251300.18722655X-RAY DIFFRACTION95
5.0795-5.81320.25571430.20262625X-RAY DIFFRACTION94
5.8132-7.31880.26741290.20862590X-RAY DIFFRACTION92
7.3188-44.86550.21371150.18262550X-RAY DIFFRACTION89

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